Starting phenix.real_space_refine on Mon Sep 23 14:09:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tly_25990/09_2024/7tly_25990.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tly_25990/09_2024/7tly_25990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tly_25990/09_2024/7tly_25990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tly_25990/09_2024/7tly_25990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tly_25990/09_2024/7tly_25990.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tly_25990/09_2024/7tly_25990.cif" } resolution = 3.0 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= 0.034 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 13 5.16 5 C 1990 2.51 5 N 534 2.21 5 O 568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3105 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 950 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 718 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1388 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.45, per 1000 atoms: 1.43 Number of scatterers: 3105 At special positions: 0 Unit cell: (69.969, 74.184, 79.242, 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 13 16.00 O 568 8.00 N 534 7.00 C 1990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 336 " - pdb=" SG CYS I 361 " distance=2.03 Simple disulfide: pdb=" SG CYS I 379 " - pdb=" SG CYS I 432 " distance=2.04 Simple disulfide: pdb=" SG CYS I 391 " - pdb=" SG CYS I 525 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " NAG C 1 " - " FUC C 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN I 343 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 400.9 milliseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 9 sheets defined 13.5% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.580A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'I' and resid 338 through 343 Processing helix chain 'I' and resid 349 through 353 removed outlier: 3.747A pdb=" N TRP I 353 " --> pdb=" O VAL I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 371 Processing helix chain 'I' and resid 386 through 389 Processing helix chain 'I' and resid 405 through 410 removed outlier: 4.432A pdb=" N ARG I 408 " --> pdb=" O ASP I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 443 Processing helix chain 'I' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.857A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.735A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11 removed outlier: 7.040A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 Processing sheet with id=AA7, first strand: chain 'I' and resid 354 through 358 removed outlier: 3.666A pdb=" N ASN I 394 " --> pdb=" O GLU I 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 361 through 362 removed outlier: 6.503A pdb=" N CYS I 361 " --> pdb=" O CYS I 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 452 through 454 126 hydrogen bonds defined for protein. 282 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: 0.96 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 709 1.33 - 1.45: 786 1.45 - 1.58: 1672 1.58 - 1.70: 2 1.70 - 1.83: 16 Bond restraints: 3185 Sorted by residual: bond pdb=" N ASN I 388 " pdb=" CA ASN I 388 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.21e+00 bond pdb=" CB ILE I 332 " pdb=" CG1 ILE I 332 " ideal model delta sigma weight residual 1.530 1.588 -0.058 2.00e-02 2.50e+03 8.41e+00 bond pdb=" N ASN I 417 " pdb=" CA ASN I 417 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.35e-02 5.49e+03 7.56e+00 bond pdb=" N PRO B 8 " pdb=" CD PRO B 8 " ideal model delta sigma weight residual 1.474 1.512 -0.038 1.40e-02 5.10e+03 7.56e+00 bond pdb=" NE ARG I 457 " pdb=" CZ ARG I 457 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.55e+00 ... (remaining 3180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 4056 2.31 - 4.62: 217 4.62 - 6.93: 52 6.93 - 9.24: 7 9.24 - 11.55: 4 Bond angle restraints: 4336 Sorted by residual: angle pdb=" N ASP I 389 " pdb=" CA ASP I 389 " pdb=" C ASP I 389 " ideal model delta sigma weight residual 112.92 123.82 -10.90 1.23e+00 6.61e-01 7.85e+01 angle pdb=" N ASP I 389 " pdb=" CA ASP I 389 " pdb=" CB ASP I 389 " ideal model delta sigma weight residual 110.56 99.78 10.78 1.46e+00 4.69e-01 5.45e+01 angle pdb=" C ILE B 59 " pdb=" N PRO B 60 " pdb=" CA PRO B 60 " ideal model delta sigma weight residual 119.78 127.10 -7.32 1.03e+00 9.43e-01 5.06e+01 angle pdb=" C ARG I 498 " pdb=" N PRO I 499 " pdb=" CA PRO I 499 " ideal model delta sigma weight residual 119.87 127.21 -7.34 1.04e+00 9.25e-01 4.98e+01 angle pdb=" C PHE I 490 " pdb=" N PRO I 491 " pdb=" CA PRO I 491 " ideal model delta sigma weight residual 119.56 126.56 -7.00 1.02e+00 9.61e-01 4.71e+01 ... (remaining 4331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 1824 21.31 - 42.61: 52 42.61 - 63.92: 8 63.92 - 85.22: 8 85.22 - 106.53: 5 Dihedral angle restraints: 1897 sinusoidal: 724 harmonic: 1173 Sorted by residual: dihedral pdb=" C ALA B 52 " pdb=" N ALA B 52 " pdb=" CA ALA B 52 " pdb=" CB ALA B 52 " ideal model delta harmonic sigma weight residual -122.60 -136.01 13.41 0 2.50e+00 1.60e-01 2.88e+01 dihedral pdb=" N SER B 53 " pdb=" C SER B 53 " pdb=" CA SER B 53 " pdb=" CB SER B 53 " ideal model delta harmonic sigma weight residual 122.80 112.34 10.46 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.32 32.68 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 1894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 383 0.096 - 0.192: 80 0.192 - 0.288: 12 0.288 - 0.384: 3 0.384 - 0.480: 1 Chirality restraints: 479 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.53e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.06e+01 chirality pdb=" CA ALA B 52 " pdb=" N ALA B 52 " pdb=" C ALA B 52 " pdb=" CB ALA B 52 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 476 not shown) Planarity restraints: 554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 461 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C LEU I 461 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU I 461 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS I 462 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 31 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C SER B 31 " 0.031 2.00e-02 2.50e+03 pdb=" O SER B 31 " -0.012 2.00e-02 2.50e+03 pdb=" N THR B 32 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 495 " -0.023 2.00e-02 2.50e+03 1.20e-02 2.87e+00 pdb=" CG TYR I 495 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR I 495 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR I 495 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR I 495 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR I 495 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR I 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 495 " -0.017 2.00e-02 2.50e+03 ... (remaining 551 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 1742 3.02 - 3.49: 2674 3.49 - 3.96: 5157 3.96 - 4.43: 5922 4.43 - 4.90: 9437 Nonbonded interactions: 24932 Sorted by model distance: nonbonded pdb=" O GLN B 6 " pdb=" OG SER B 7 " model vdw 2.556 3.040 nonbonded pdb=" OD1 ASP A 115 " pdb=" N ASN A 116 " model vdw 2.586 3.120 nonbonded pdb=" N ASP I 428 " pdb=" OD1 ASP I 428 " model vdw 2.591 3.120 nonbonded pdb=" N LEU I 387 " pdb=" N ASN I 388 " model vdw 2.592 2.560 nonbonded pdb=" N LYS I 462 " pdb=" O LYS I 462 " model vdw 2.611 2.496 ... (remaining 24927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 6.830 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.140 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.010 0.058 3185 Z= 0.665 Angle : 1.320 11.553 4336 Z= 0.895 Chirality : 0.083 0.480 479 Planarity : 0.005 0.025 553 Dihedral : 12.976 106.526 1138 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 5.56 % 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: 0.36 (0.41), residues: 396 helix: -3.25 (0.69), residues: 33 sheet: 0.71 (0.40), residues: 157 loop : 0.65 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 50 HIS 0.002 0.001 HIS B 92 PHE 0.013 0.003 PHE B 98 TYR 0.023 0.003 TYR I 495 ARG 0.003 0.000 ARG I 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.5815 (m-30) cc_final: 0.5444 (m-30) REVERT: A 95 TYR cc_start: 0.7806 (m-80) cc_final: 0.7444 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 1.1110 time to fit residues: 73.2084 Evaluate side-chains 42 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 chunk 20 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 36 optimal weight: 0.0980 chunk 11 optimal weight: 0.4980 overall best weight: 0.0956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3185 Z= 0.147 Angle : 0.524 7.022 4336 Z= 0.279 Chirality : 0.044 0.172 479 Planarity : 0.005 0.047 553 Dihedral : 8.449 63.038 531 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.81 % Allowed : 10.18 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.34 (0.41), residues: 396 helix: -2.95 (0.77), residues: 33 sheet: 0.91 (0.41), residues: 153 loop : 0.37 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 117 HIS 0.003 0.001 HIS B 92 PHE 0.009 0.001 PHE B 98 TYR 0.008 0.001 TYR I 369 ARG 0.002 0.000 ARG I 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 43 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6555 (mm-40) REVERT: A 90 ASP cc_start: 0.6198 (m-30) cc_final: 0.5787 (m-30) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 1.2638 time to fit residues: 64.9771 Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 43 GLN Chi-restraints excluded: chain I residue 332 ILE Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.0170 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3185 Z= 0.307 Angle : 0.635 11.021 4336 Z= 0.320 Chirality : 0.048 0.152 479 Planarity : 0.006 0.054 553 Dihedral : 5.909 40.171 531 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.46 % Allowed : 11.23 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 396 helix: -2.58 (0.95), residues: 26 sheet: 0.67 (0.41), residues: 150 loop : -0.20 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 50 HIS 0.003 0.002 HIS B 92 PHE 0.017 0.002 PHE I 429 TYR 0.016 0.002 TYR A 95 ARG 0.003 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.351 Fit side-chains REVERT: A 59 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7366 (t0) REVERT: B 94 THR cc_start: 0.8678 (m) cc_final: 0.8395 (m) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 1.3110 time to fit residues: 64.9115 Evaluate side-chains 47 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.0170 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 34 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3185 Z= 0.250 Angle : 0.599 9.941 4336 Z= 0.302 Chirality : 0.046 0.146 479 Planarity : 0.005 0.051 553 Dihedral : 4.785 31.133 531 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.86 % Allowed : 11.58 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.45 (0.40), residues: 396 helix: -3.12 (0.78), residues: 32 sheet: 0.60 (0.42), residues: 140 loop : -0.39 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 50 HIS 0.003 0.001 HIS B 92 PHE 0.011 0.002 PHE I 429 TYR 0.023 0.002 TYR A 95 ARG 0.004 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.359 Fit side-chains REVERT: A 59 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7498 (t0) REVERT: A 119 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.6368 (pm20) REVERT: I 457 ARG cc_start: 0.8035 (ttt90) cc_final: 0.7624 (ttt90) outliers start: 11 outliers final: 5 residues processed: 46 average time/residue: 1.3147 time to fit residues: 62.2326 Evaluate side-chains 46 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 7 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3185 Z= 0.141 Angle : 0.501 8.525 4336 Z= 0.254 Chirality : 0.043 0.142 479 Planarity : 0.005 0.048 553 Dihedral : 4.162 19.916 531 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.46 % Allowed : 12.98 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.28 (0.40), residues: 396 helix: -2.81 (0.91), residues: 26 sheet: 0.71 (0.42), residues: 141 loop : -0.40 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 436 HIS 0.002 0.001 HIS B 92 PHE 0.006 0.001 PHE I 374 TYR 0.019 0.001 TYR A 95 ARG 0.003 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.349 Fit side-chains REVERT: A 32 TYR cc_start: 0.8329 (m-80) cc_final: 0.8022 (m-80) REVERT: A 90 ASP cc_start: 0.6270 (m-30) cc_final: 0.5880 (m-30) REVERT: I 457 ARG cc_start: 0.8023 (ttt90) cc_final: 0.7563 (ttt90) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 1.2367 time to fit residues: 59.8315 Evaluate side-chains 45 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3185 Z= 0.344 Angle : 0.635 10.872 4336 Z= 0.321 Chirality : 0.047 0.148 479 Planarity : 0.006 0.051 553 Dihedral : 4.640 18.546 531 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.86 % Allowed : 12.63 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.79 (0.39), residues: 396 helix: -3.27 (0.76), residues: 32 sheet: 0.49 (0.42), residues: 141 loop : -0.74 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 36 HIS 0.003 0.001 HIS B 92 PHE 0.013 0.002 PHE I 429 TYR 0.022 0.002 TYR A 95 ARG 0.005 0.001 ARG I 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.297 Fit side-chains REVERT: A 90 ASP cc_start: 0.6455 (m-30) cc_final: 0.5869 (m-30) REVERT: A 119 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.6664 (pm20) REVERT: I 346 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.7200 (ttm-80) outliers start: 11 outliers final: 10 residues processed: 49 average time/residue: 1.1803 time to fit residues: 59.5717 Evaluate side-chains 52 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 493 ARG Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 38 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3185 Z= 0.189 Angle : 0.522 8.986 4336 Z= 0.266 Chirality : 0.044 0.132 479 Planarity : 0.005 0.056 553 Dihedral : 4.146 17.783 531 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.21 % Allowed : 11.93 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.83 (0.40), residues: 396 helix: -3.34 (0.73), residues: 32 sheet: 0.53 (0.44), residues: 140 loop : -0.81 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 50 HIS 0.002 0.001 HIS B 92 PHE 0.007 0.001 PHE I 392 TYR 0.019 0.001 TYR A 95 ARG 0.006 0.001 ARG I 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.359 Fit side-chains REVERT: A 90 ASP cc_start: 0.6326 (m-30) cc_final: 0.6025 (m-30) REVERT: A 119 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6567 (pm20) REVERT: I 346 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7165 (mtm-85) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 1.2545 time to fit residues: 61.9280 Evaluate side-chains 51 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 493 ARG Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 chunk 28 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 354 ASN ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3185 Z= 0.226 Angle : 0.554 9.649 4336 Z= 0.279 Chirality : 0.045 0.137 479 Planarity : 0.006 0.056 553 Dihedral : 4.181 17.675 531 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.86 % Allowed : 12.28 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.40), residues: 396 helix: -3.33 (0.73), residues: 32 sheet: 0.51 (0.44), residues: 142 loop : -0.85 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 50 HIS 0.002 0.001 HIS B 92 PHE 0.008 0.001 PHE I 429 TYR 0.020 0.001 TYR A 95 ARG 0.006 0.001 ARG I 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.323 Fit side-chains REVERT: A 90 ASP cc_start: 0.6383 (m-30) cc_final: 0.5914 (m-30) REVERT: A 119 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.6576 (pm20) REVERT: I 346 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7200 (mtm-85) outliers start: 11 outliers final: 10 residues processed: 46 average time/residue: 1.2329 time to fit residues: 58.4528 Evaluate side-chains 49 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 493 ARG Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3185 Z= 0.278 Angle : 0.586 10.687 4336 Z= 0.296 Chirality : 0.046 0.139 479 Planarity : 0.006 0.053 553 Dihedral : 4.360 17.944 531 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.56 % Allowed : 11.93 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.40), residues: 396 helix: -3.37 (0.71), residues: 33 sheet: 0.44 (0.44), residues: 142 loop : -0.98 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 50 HIS 0.003 0.001 HIS B 92 PHE 0.011 0.001 PHE I 392 TYR 0.021 0.002 TYR A 95 ARG 0.006 0.001 ARG I 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.373 Fit side-chains REVERT: A 90 ASP cc_start: 0.6556 (m-30) cc_final: 0.6093 (m-30) REVERT: A 119 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.6602 (pm20) REVERT: I 346 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7205 (mtm-85) outliers start: 13 outliers final: 10 residues processed: 48 average time/residue: 1.1942 time to fit residues: 59.1148 Evaluate side-chains 49 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 493 ARG Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3185 Z= 0.389 Angle : 0.686 11.612 4336 Z= 0.345 Chirality : 0.049 0.158 479 Planarity : 0.006 0.055 553 Dihedral : 4.860 18.880 531 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.91 % Allowed : 11.23 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.39), residues: 396 helix: -3.42 (0.70), residues: 33 sheet: 0.18 (0.43), residues: 144 loop : -1.28 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 50 HIS 0.004 0.002 HIS B 92 PHE 0.012 0.002 PHE I 429 TYR 0.022 0.002 TYR A 95 ARG 0.006 0.001 ARG B 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.347 Fit side-chains REVERT: A 90 ASP cc_start: 0.6565 (m-30) cc_final: 0.6044 (m-30) REVERT: A 119 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: B 24 ARG cc_start: 0.7471 (tpp80) cc_final: 0.7237 (tpp80) REVERT: I 346 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7223 (mtm-85) outliers start: 14 outliers final: 12 residues processed: 48 average time/residue: 1.2016 time to fit residues: 59.4954 Evaluate side-chains 48 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 493 ARG Chi-restraints excluded: chain I residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 354 ASN ** I 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.159937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.150746 restraints weight = 4101.737| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.10 r_work: 0.3541 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3185 Z= 0.182 Angle : 0.531 8.917 4336 Z= 0.270 Chirality : 0.044 0.130 479 Planarity : 0.005 0.051 553 Dihedral : 4.208 17.585 531 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.86 % Allowed : 13.68 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.39), residues: 396 helix: -3.43 (0.69), residues: 33 sheet: 0.37 (0.44), residues: 140 loop : -1.23 (0.36), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 117 HIS 0.002 0.001 HIS B 92 PHE 0.008 0.001 PHE I 392 TYR 0.019 0.001 TYR A 95 ARG 0.008 0.001 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.87 seconds wall clock time: 36 minutes 18.34 seconds (2178.34 seconds total)