Starting phenix.real_space_refine on Sun Mar 10 16:06:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwo_30485/03_2024/7cwo_30485.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwo_30485/03_2024/7cwo_30485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwo_30485/03_2024/7cwo_30485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwo_30485/03_2024/7cwo_30485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwo_30485/03_2024/7cwo_30485.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwo_30485/03_2024/7cwo_30485.pdb" } resolution = 3.9 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 14 5.16 5 C 2063 2.51 5 N 558 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" 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: 3254 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1519 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Time building chain proxies: 2.22, per 1000 atoms: 0.68 Number of scatterers: 3254 At special positions: 0 Unit cell: (84.24, 70.72, 84.24, 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 14 16.00 O 619 8.00 N 558 7.00 C 2063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 599.1 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 7 sheets defined 10.7% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.952A 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 502 through 506 removed outlier: 3.675A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 201 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: 0.81 Time building geometry restraints manager: 1.34 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: 1028 1.34 - 1.46: 879 1.46 - 1.58: 1411 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3334 Sorted by residual: bond pdb=" C VAL H 12 " pdb=" N GLN H 13 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.47e-02 4.63e+03 6.43e+00 bond pdb=" C VAL A 433 " pdb=" N ILE A 434 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.26e-02 6.30e+03 4.60e+00 bond pdb=" C SER L 93 " pdb=" N THR L 94 " ideal model delta sigma weight residual 1.332 1.296 0.036 1.92e-02 2.71e+03 3.54e+00 bond pdb=" CG GLN L 89 " pdb=" CD GLN L 89 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.81e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.447 0.051 3.10e-02 1.04e+03 2.67e+00 ... (remaining 3329 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.94: 79 105.94 - 112.97: 1696 112.97 - 120.00: 1112 120.00 - 127.03: 1603 127.03 - 134.06: 39 Bond angle restraints: 4529 Sorted by residual: angle pdb=" C PHE A 486 " pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 angle pdb=" C GLN L 38 " pdb=" N LYS L 39 " pdb=" CA LYS L 39 " ideal model delta sigma weight residual 120.49 114.65 5.84 1.42e+00 4.96e-01 1.69e+01 angle pdb=" N VAL A 382 " pdb=" CA VAL A 382 " pdb=" C VAL A 382 " ideal model delta sigma weight residual 108.23 103.40 4.83 1.43e+00 4.89e-01 1.14e+01 angle pdb=" N MET H 103 " pdb=" CA MET H 103 " pdb=" C MET H 103 " ideal model delta sigma weight residual 112.93 108.70 4.23 1.33e+00 5.65e-01 1.01e+01 angle pdb=" C PRO A 463 " pdb=" N PHE A 464 " pdb=" CA PHE A 464 " ideal model delta sigma weight residual 123.05 127.97 -4.92 1.57e+00 4.06e-01 9.81e+00 ... (remaining 4524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.80: 1685 9.80 - 19.60: 223 19.60 - 29.40: 43 29.40 - 39.20: 12 39.20 - 49.00: 7 Dihedral angle restraints: 1970 sinusoidal: 749 harmonic: 1221 Sorted by residual: dihedral pdb=" CA ARG H 72 " pdb=" C ARG H 72 " pdb=" N ASP H 73 " pdb=" CA ASP H 73 " ideal model delta harmonic sigma weight residual 180.00 141.51 38.49 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -146.21 -33.79 0 5.00e+00 4.00e-02 4.57e+01 dihedral pdb=" CA ARG H 87 " pdb=" C ARG H 87 " pdb=" N ALA H 88 " pdb=" CA ALA H 88 " ideal model delta harmonic sigma weight residual 180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 1967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 306 0.047 - 0.093: 139 0.093 - 0.140: 34 0.140 - 0.187: 10 0.187 - 0.233: 1 Chirality restraints: 490 Sorted by residual: chirality pdb=" CG LEU H 79 " pdb=" CB LEU H 79 " pdb=" CD1 LEU H 79 " pdb=" CD2 LEU H 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL A 350 " pdb=" CA VAL A 350 " pdb=" CG1 VAL A 350 " pdb=" CG2 VAL A 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 487 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO L 59 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 392 " -0.017 2.00e-02 2.50e+03 1.54e-02 4.12e+00 pdb=" CG PHE A 392 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 392 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 392 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 392 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 392 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 392 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 101 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C THR H 101 " 0.034 2.00e-02 2.50e+03 pdb=" O THR H 101 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU H 102 " -0.011 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 832 2.79 - 3.32: 2933 3.32 - 3.84: 5385 3.84 - 4.37: 6236 4.37 - 4.90: 10594 Nonbonded interactions: 25980 Sorted by model distance: nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.262 2.440 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.301 2.440 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR A 393 " pdb=" OD1 ASN A 394 " model vdw 2.326 2.440 ... (remaining 25975 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 1.810 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.850 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.007 0.060 3334 Z= 0.422 Angle : 1.044 10.573 4529 Z= 0.603 Chirality : 0.057 0.233 490 Planarity : 0.007 0.052 585 Dihedral : 9.374 43.259 1178 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.28 % Allowed : 1.14 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.36), residues: 416 helix: -4.84 (0.54), residues: 15 sheet: -2.29 (0.40), residues: 141 loop : -2.51 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 47 HIS 0.005 0.002 HIS A 519 PHE 0.035 0.004 PHE A 392 TYR 0.030 0.003 TYR H 94 ARG 0.013 0.001 ARG L 61 *********************** 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 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.6843 (mttp) cc_final: 0.6276 (tttt) REVERT: H 45 LEU cc_start: 0.7485 (mt) cc_final: 0.7000 (mt) REVERT: H 72 ARG cc_start: 0.7856 (ptt90) cc_final: 0.7263 (ptp-110) REVERT: L 4 LEU cc_start: 0.8811 (mt) cc_final: 0.8527 (mm) REVERT: L 11 LEU cc_start: 0.7856 (tt) cc_final: 0.7409 (mt) REVERT: L 82 ASP cc_start: 0.8034 (m-30) cc_final: 0.7114 (t0) REVERT: L 104 VAL cc_start: 0.8817 (t) cc_final: 0.8450 (p) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.2029 time to fit residues: 27.3034 Evaluate side-chains 66 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN H 35 HIS H 84 ASN H 104 ASN H 105 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 3334 Z= 0.309 Angle : 0.725 8.012 4529 Z= 0.376 Chirality : 0.046 0.187 490 Planarity : 0.005 0.040 585 Dihedral : 7.015 32.497 468 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 3.42 % Allowed : 11.97 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.38), residues: 416 helix: -4.30 (0.63), residues: 21 sheet: -1.75 (0.42), residues: 129 loop : -2.36 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 35 HIS 0.003 0.002 HIS H 99 PHE 0.013 0.002 PHE A 342 TYR 0.018 0.002 TYR H 53 ARG 0.007 0.001 ARG H 67 *********************** 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 86 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.6902 (mttp) cc_final: 0.6618 (tttt) REVERT: A 492 LEU cc_start: 0.8754 (mm) cc_final: 0.8419 (mt) REVERT: A 524 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8499 (p) REVERT: H 72 ARG cc_start: 0.7558 (ptt90) cc_final: 0.7315 (ptp-110) REVERT: L 104 VAL cc_start: 0.8674 (t) cc_final: 0.8454 (p) outliers start: 12 outliers final: 6 residues processed: 81 average time/residue: 0.1767 time to fit residues: 17.0063 Evaluate side-chains 69 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 0.0270 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 overall best weight: 3.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3334 Z= 0.278 Angle : 0.680 7.926 4529 Z= 0.350 Chirality : 0.045 0.184 490 Planarity : 0.005 0.037 585 Dihedral : 6.470 30.242 468 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.56 % Allowed : 14.53 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.37), residues: 416 helix: -4.40 (0.53), residues: 21 sheet: -1.39 (0.42), residues: 127 loop : -2.26 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 35 HIS 0.004 0.002 HIS H 99 PHE 0.016 0.002 PHE A 392 TYR 0.019 0.002 TYR L 87 ARG 0.005 0.001 ARG H 16 *********************** 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 83 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 72 ARG cc_start: 0.7620 (ptt90) cc_final: 0.7282 (ptp-110) REVERT: L 81 GLU cc_start: 0.7603 (pm20) cc_final: 0.7344 (pm20) REVERT: L 104 VAL cc_start: 0.8524 (t) cc_final: 0.8244 (p) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.1787 time to fit residues: 16.4595 Evaluate side-chains 66 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 0.0980 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN L 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3334 Z= 0.134 Angle : 0.623 8.981 4529 Z= 0.309 Chirality : 0.044 0.166 490 Planarity : 0.004 0.034 585 Dihedral : 5.428 24.225 467 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.42 % Allowed : 17.09 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.38), residues: 416 helix: -4.54 (0.56), residues: 15 sheet: -1.18 (0.40), residues: 144 loop : -2.00 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.017 0.001 PHE A 392 TYR 0.024 0.001 TYR L 92 ARG 0.005 0.001 ARG A 454 *********************** 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 87 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5674 (m-30) cc_final: 0.5448 (m-30) REVERT: L 81 GLU cc_start: 0.7602 (pm20) cc_final: 0.7266 (pm20) outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 0.1449 time to fit residues: 14.4636 Evaluate side-chains 64 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 0.0170 chunk 7 optimal weight: 4.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 3334 Z= 0.367 Angle : 0.766 13.608 4529 Z= 0.388 Chirality : 0.045 0.151 490 Planarity : 0.004 0.033 585 Dihedral : 6.116 28.316 467 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 5.13 % Allowed : 18.52 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.38), residues: 416 helix: -4.26 (0.78), residues: 15 sheet: -1.14 (0.42), residues: 137 loop : -1.95 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 35 HIS 0.005 0.002 HIS H 99 PHE 0.024 0.003 PHE H 27 TYR 0.018 0.002 TYR H 53 ARG 0.005 0.001 ARG H 67 *********************** 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 79 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8650 (mm) cc_final: 0.8368 (mt) REVERT: H 54 ASP cc_start: 0.5719 (m-30) cc_final: 0.5516 (m-30) outliers start: 18 outliers final: 14 residues processed: 69 average time/residue: 0.1763 time to fit residues: 14.6487 Evaluate side-chains 68 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 0.0050 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3334 Z= 0.321 Angle : 0.741 11.866 4529 Z= 0.374 Chirality : 0.046 0.207 490 Planarity : 0.004 0.035 585 Dihedral : 6.157 27.414 467 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 5.70 % Allowed : 18.80 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.38), residues: 416 helix: -4.32 (0.70), residues: 15 sheet: -1.14 (0.42), residues: 137 loop : -1.93 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 35 HIS 0.005 0.002 HIS H 99 PHE 0.020 0.002 PHE H 27 TYR 0.033 0.002 TYR L 92 ARG 0.005 0.001 ARG L 24 *********************** 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 79 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8611 (mm) cc_final: 0.8346 (mt) REVERT: H 54 ASP cc_start: 0.5540 (m-30) cc_final: 0.5319 (m-30) outliers start: 20 outliers final: 14 residues processed: 68 average time/residue: 0.1228 time to fit residues: 10.7699 Evaluate side-chains 70 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 0.0970 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3334 Z= 0.261 Angle : 0.726 14.214 4529 Z= 0.358 Chirality : 0.046 0.206 490 Planarity : 0.004 0.036 585 Dihedral : 5.880 26.103 467 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.56 % Allowed : 20.51 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.38), residues: 416 helix: -4.27 (0.73), residues: 15 sheet: -1.01 (0.43), residues: 137 loop : -1.87 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 35 HIS 0.003 0.002 HIS H 99 PHE 0.016 0.002 PHE H 27 TYR 0.028 0.002 TYR L 92 ARG 0.004 0.001 ARG L 24 *********************** 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 75 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8583 (mm) cc_final: 0.8299 (mt) REVERT: H 54 ASP cc_start: 0.5510 (m-30) cc_final: 0.5093 (m-30) REVERT: L 81 GLU cc_start: 0.7526 (pm20) cc_final: 0.7269 (pm20) outliers start: 16 outliers final: 14 residues processed: 66 average time/residue: 0.1441 time to fit residues: 11.8895 Evaluate side-chains 67 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3334 Z= 0.175 Angle : 0.714 14.258 4529 Z= 0.343 Chirality : 0.045 0.194 490 Planarity : 0.004 0.036 585 Dihedral : 5.218 20.707 467 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.99 % Allowed : 20.80 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.39), residues: 416 helix: -4.32 (0.66), residues: 15 sheet: -1.06 (0.40), residues: 156 loop : -1.57 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 35 HIS 0.003 0.001 HIS H 99 PHE 0.012 0.001 PHE L 62 TYR 0.028 0.001 TYR L 92 ARG 0.007 0.001 ARG L 24 *********************** 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 76 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8641 (mm) cc_final: 0.8353 (mt) REVERT: H 54 ASP cc_start: 0.5303 (m-30) cc_final: 0.4881 (m-30) REVERT: L 81 GLU cc_start: 0.7378 (pm20) cc_final: 0.7105 (pm20) outliers start: 14 outliers final: 13 residues processed: 70 average time/residue: 0.1223 time to fit residues: 11.0601 Evaluate side-chains 72 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3334 Z= 0.314 Angle : 0.753 14.253 4529 Z= 0.370 Chirality : 0.046 0.200 490 Planarity : 0.004 0.039 585 Dihedral : 5.801 25.398 467 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.13 % Allowed : 19.94 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.39), residues: 416 helix: -4.17 (0.81), residues: 15 sheet: -0.85 (0.42), residues: 143 loop : -1.61 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.021 0.002 PHE H 27 TYR 0.019 0.002 TYR L 92 ARG 0.008 0.001 ARG L 24 *********************** 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 75 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8638 (mm) cc_final: 0.8368 (mt) REVERT: H 54 ASP cc_start: 0.5523 (m-30) cc_final: 0.5078 (m-30) REVERT: L 81 GLU cc_start: 0.7467 (pm20) cc_final: 0.7224 (pm20) outliers start: 18 outliers final: 15 residues processed: 67 average time/residue: 0.1122 time to fit residues: 10.0159 Evaluate side-chains 71 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 20.0000 chunk 3 optimal weight: 0.0970 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3334 Z= 0.186 Angle : 0.711 14.644 4529 Z= 0.339 Chirality : 0.045 0.195 490 Planarity : 0.004 0.034 585 Dihedral : 5.327 21.190 467 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.99 % Allowed : 21.37 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.39), residues: 416 helix: -4.26 (0.70), residues: 15 sheet: -1.00 (0.40), residues: 158 loop : -1.49 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.008 0.001 PHE H 27 TYR 0.023 0.001 TYR L 92 ARG 0.007 0.001 ARG L 24 ********************** 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 71 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8589 (mm) cc_final: 0.8303 (mt) REVERT: H 54 ASP cc_start: 0.5276 (m-30) cc_final: 0.4780 (m-30) REVERT: L 81 GLU cc_start: 0.7292 (pm20) cc_final: 0.7057 (pm20) outliers start: 14 outliers final: 13 residues processed: 65 average time/residue: 0.1412 time to fit residues: 11.6276 Evaluate side-chains 67 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.080870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070951 restraints weight = 14644.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.072856 restraints weight = 8319.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.074158 restraints weight = 5451.459| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3334 Z= 0.266 Angle : 0.731 14.947 4529 Z= 0.356 Chirality : 0.045 0.199 490 Planarity : 0.004 0.043 585 Dihedral : 5.582 23.776 467 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.70 % Allowed : 21.65 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.40), residues: 416 helix: -4.15 (0.80), residues: 15 sheet: -1.02 (0.40), residues: 158 loop : -1.58 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP L 35 HIS 0.004 0.002 HIS H 35 PHE 0.016 0.002 PHE H 27 TYR 0.018 0.002 TYR L 92 ARG 0.007 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1084.96 seconds wall clock time: 20 minutes 22.95 seconds (1222.95 seconds total)