Starting phenix.real_space_refine on Sat Apr 6 01:08:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x91_33063/04_2024/7x91_33063_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x91_33063/04_2024/7x91_33063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x91_33063/04_2024/7x91_33063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x91_33063/04_2024/7x91_33063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x91_33063/04_2024/7x91_33063_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x91_33063/04_2024/7x91_33063_trim.pdb" } resolution = 4.3 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: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2137 2.51 5 N 560 2.21 5 O 652 1.98 5 H 3196 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "L GLU 55": "OE1" <-> "OE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6559 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3094 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "H" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1834 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1603 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.53, per 1000 atoms: 0.54 Number of scatterers: 6559 At special positions: 0 Unit cell: (85.387, 96.164, 81.242, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 652 8.00 N 560 7.00 C 2137 6.00 H 3196 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 667.0 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 7 sheets defined 4.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.068A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.611A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.615A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) 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: 3.682A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.681A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 59 through 60 removed outlier: 4.148A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TRP H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.031A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3193 1.03 - 1.23: 8 1.23 - 1.42: 1510 1.42 - 1.62: 1920 1.62 - 1.81: 15 Bond restraints: 6646 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" N GLU H 1 " pdb=" H GLU H 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.19e+00 ... (remaining 6641 not shown) Histogram of bond angle deviations from ideal: 100.98 - 107.58: 374 107.58 - 114.18: 7491 114.18 - 120.78: 2265 120.78 - 127.38: 1752 127.38 - 133.98: 36 Bond angle restraints: 11918 Sorted by residual: angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 110.70 113.67 -2.97 1.22e+00 6.72e-01 5.91e+00 angle pdb=" CA PRO L 95 " pdb=" C PRO L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 117.93 120.78 -2.85 1.20e+00 6.94e-01 5.64e+00 angle pdb=" N GLY H 8 " pdb=" CA GLY H 8 " pdb=" C GLY H 8 " ideal model delta sigma weight residual 112.34 116.84 -4.50 2.04e+00 2.40e-01 4.88e+00 angle pdb=" N GLY A 381 " pdb=" CA GLY A 381 " pdb=" C GLY A 381 " ideal model delta sigma weight residual 115.08 112.69 2.39 1.19e+00 7.06e-01 4.05e+00 angle pdb=" CA CYS L 88 " pdb=" CB CYS L 88 " pdb=" SG CYS L 88 " ideal model delta sigma weight residual 114.40 118.93 -4.53 2.30e+00 1.89e-01 3.89e+00 ... (remaining 11913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2898 17.76 - 35.53: 265 35.53 - 53.29: 55 53.29 - 71.06: 22 71.06 - 88.82: 6 Dihedral angle restraints: 3246 sinusoidal: 1739 harmonic: 1507 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 150.68 -57.68 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CA SER H 75 " pdb=" C SER H 75 " pdb=" N THR H 76 " pdb=" CA THR H 76 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ALA L 92 " pdb=" C ALA L 92 " pdb=" N ASN L 93 " pdb=" CA ASN L 93 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 3243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 299 0.032 - 0.064: 139 0.064 - 0.096: 43 0.096 - 0.128: 26 0.128 - 0.160: 7 Chirality restraints: 514 Sorted by residual: chirality pdb=" CA ILE L 39 " pdb=" N ILE L 39 " pdb=" C ILE L 39 " pdb=" CB ILE L 39 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 511 not shown) Planarity restraints: 1010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " -0.020 2.00e-02 2.50e+03 1.30e-02 6.71e+00 pdb=" CG TRP H 36 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP H 36 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP H 36 " -0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP H 36 " 0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 36 " 0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 36 " -0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP H 36 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 73 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" CG ASP H 73 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP H 73 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP H 73 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE L 39 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO L 40 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " -0.017 5.00e-02 4.00e+02 ... (remaining 1007 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 357 2.17 - 2.78: 12569 2.78 - 3.38: 17088 3.38 - 3.99: 22024 3.99 - 4.60: 33342 Nonbonded interactions: 85380 Sorted by model distance: nonbonded pdb=" O VAL H 52 " pdb="HH21 ARG H 72 " model vdw 1.559 1.850 nonbonded pdb="HH21 ARG H 67 " pdb=" O SER H 85 " model vdw 1.632 1.850 nonbonded pdb=" OD1 ASP L 106 " pdb=" H ILE L 107 " model vdw 1.693 1.850 nonbonded pdb=" OE1 GLU A 340 " pdb=" H GLU A 340 " model vdw 1.707 1.850 nonbonded pdb=" OG SER A 349 " pdb=" H LEU A 452 " model vdw 1.708 1.850 ... (remaining 85375 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 1.190 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.360 Find NCS groups from input model: 0.110 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.003 0.033 3450 Z= 0.197 Angle : 0.626 7.597 4699 Z= 0.335 Chirality : 0.046 0.160 514 Planarity : 0.003 0.030 609 Dihedral : 14.403 88.821 1261 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.38), residues: 421 helix: -3.86 (0.64), residues: 24 sheet: -0.91 (0.48), residues: 117 loop : -2.10 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 36 HIS 0.004 0.003 HIS A 519 PHE 0.011 0.001 PHE L 99 TYR 0.011 0.001 TYR A 453 ARG 0.001 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7342 (mm-30) REVERT: H 80 TYR cc_start: 0.8271 (m-80) cc_final: 0.7786 (m-10) REVERT: L 32 ASN cc_start: 0.7872 (m-40) cc_final: 0.7627 (m-40) REVERT: L 53 ASN cc_start: 0.8995 (t0) cc_final: 0.8747 (t0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.5140 time to fit residues: 55.9263 Evaluate side-chains 66 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 40.0000 chunk 11 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3450 Z= 0.271 Angle : 0.612 7.119 4699 Z= 0.320 Chirality : 0.043 0.147 514 Planarity : 0.005 0.055 609 Dihedral : 6.316 54.816 511 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 0.27 % Allowed : 3.27 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.38), residues: 421 helix: -3.16 (0.90), residues: 24 sheet: -0.99 (0.46), residues: 121 loop : -2.12 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.003 0.002 HIS A 519 PHE 0.024 0.002 PHE A 377 TYR 0.012 0.002 TYR A 449 ARG 0.010 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7262 (mm-30) REVERT: H 80 TYR cc_start: 0.8281 (m-80) cc_final: 0.7847 (m-10) REVERT: H 83 LEU cc_start: 0.9241 (pp) cc_final: 0.8996 (pp) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.5202 time to fit residues: 40.6436 Evaluate side-chains 54 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN H 59 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.003 0.027 3450 Z= 0.220 Angle : 0.564 6.756 4699 Z= 0.294 Chirality : 0.043 0.137 514 Planarity : 0.004 0.035 609 Dihedral : 6.140 54.149 511 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 0.27 % Allowed : 2.18 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.38), residues: 421 helix: -3.13 (0.89), residues: 24 sheet: -0.80 (0.46), residues: 121 loop : -2.14 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.001 HIS A 519 PHE 0.018 0.001 PHE L 71 TYR 0.015 0.001 TYR A 449 ARG 0.004 0.000 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7387 (mm-30) REVERT: H 63 LYS cc_start: 0.9105 (mptt) cc_final: 0.8733 (mptt) REVERT: H 80 TYR cc_start: 0.8273 (m-80) cc_final: 0.7824 (m-10) outliers start: 1 outliers final: 1 residues processed: 67 average time/residue: 0.5302 time to fit residues: 40.4302 Evaluate side-chains 53 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 36 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3450 Z= 0.183 Angle : 0.553 6.635 4699 Z= 0.283 Chirality : 0.043 0.142 514 Planarity : 0.005 0.064 609 Dihedral : 5.887 54.015 511 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.38), residues: 421 helix: -3.07 (0.89), residues: 24 sheet: -0.82 (0.47), residues: 123 loop : -2.01 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.001 HIS A 519 PHE 0.014 0.001 PHE L 71 TYR 0.010 0.001 TYR A 449 ARG 0.005 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7431 (mm-30) REVERT: H 80 TYR cc_start: 0.8313 (m-80) cc_final: 0.7834 (m-10) REVERT: H 99 PHE cc_start: 0.8519 (m-80) cc_final: 0.8298 (m-10) REVERT: L 86 TYR cc_start: 0.8662 (m-10) cc_final: 0.8335 (m-10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.4987 time to fit residues: 37.1887 Evaluate side-chains 57 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3450 Z= 0.208 Angle : 0.559 6.540 4699 Z= 0.286 Chirality : 0.043 0.139 514 Planarity : 0.004 0.032 609 Dihedral : 5.847 54.064 511 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.39), residues: 421 helix: -2.95 (0.94), residues: 24 sheet: -0.49 (0.48), residues: 125 loop : -2.13 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.001 0.001 HIS A 519 PHE 0.016 0.001 PHE A 400 TYR 0.010 0.001 TYR H 80 ARG 0.005 0.000 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7583 (mm-30) REVERT: H 80 TYR cc_start: 0.8270 (m-80) cc_final: 0.7800 (m-10) REVERT: H 99 PHE cc_start: 0.8545 (m-80) cc_final: 0.8337 (m-10) REVERT: L 32 ASN cc_start: 0.8491 (m110) cc_final: 0.8288 (m-40) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.5301 time to fit residues: 37.2703 Evaluate side-chains 52 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3450 Z= 0.259 Angle : 0.585 6.555 4699 Z= 0.304 Chirality : 0.043 0.129 514 Planarity : 0.005 0.073 609 Dihedral : 5.936 53.910 511 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.39), residues: 421 helix: -2.02 (1.26), residues: 18 sheet: -0.46 (0.50), residues: 117 loop : -1.95 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.012 0.002 PHE L 71 TYR 0.011 0.001 TYR H 103 ARG 0.010 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 63 LYS cc_start: 0.9187 (mptt) cc_final: 0.8803 (mptt) REVERT: H 80 TYR cc_start: 0.8266 (m-80) cc_final: 0.7813 (m-10) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.4972 time to fit residues: 32.6553 Evaluate side-chains 44 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3450 Z= 0.204 Angle : 0.556 6.348 4699 Z= 0.285 Chirality : 0.043 0.139 514 Planarity : 0.004 0.035 609 Dihedral : 5.780 54.033 511 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.30 % Favored : 86.70 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.40), residues: 421 helix: -1.90 (1.31), residues: 18 sheet: -0.57 (0.48), residues: 119 loop : -1.78 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.001 PHE L 71 TYR 0.011 0.001 TYR H 80 ARG 0.003 0.000 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7597 (mm-30) REVERT: H 80 TYR cc_start: 0.8254 (m-80) cc_final: 0.7822 (m-10) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.5169 time to fit residues: 34.0642 Evaluate side-chains 47 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 50.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3450 Z= 0.251 Angle : 0.617 10.555 4699 Z= 0.321 Chirality : 0.044 0.154 514 Planarity : 0.006 0.086 609 Dihedral : 5.954 53.889 511 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.40), residues: 421 helix: -1.99 (1.27), residues: 19 sheet: -0.50 (0.47), residues: 127 loop : -1.78 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.000 0.000 HIS A 519 PHE 0.031 0.002 PHE L 73 TYR 0.010 0.001 TYR L 36 ARG 0.011 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 TYR cc_start: 0.8304 (m-80) cc_final: 0.7847 (m-10) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.4967 time to fit residues: 33.7352 Evaluate side-chains 45 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3450 Z= 0.186 Angle : 0.565 6.206 4699 Z= 0.291 Chirality : 0.044 0.160 514 Planarity : 0.004 0.051 609 Dihedral : 5.802 54.041 511 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.40), residues: 421 helix: -2.04 (1.24), residues: 19 sheet: -0.40 (0.48), residues: 127 loop : -1.65 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.001 0.001 HIS A 519 PHE 0.017 0.001 PHE L 73 TYR 0.010 0.001 TYR H 80 ARG 0.005 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 TYR cc_start: 0.8266 (m-80) cc_final: 0.7819 (m-10) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.4869 time to fit residues: 31.2693 Evaluate side-chains 51 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3450 Z= 0.214 Angle : 0.566 6.204 4699 Z= 0.293 Chirality : 0.044 0.159 514 Planarity : 0.004 0.043 609 Dihedral : 5.791 53.810 511 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.40), residues: 421 helix: -1.97 (1.27), residues: 19 sheet: -0.32 (0.48), residues: 123 loop : -1.68 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.012 0.001 PHE L 73 TYR 0.009 0.001 TYR H 80 ARG 0.005 0.001 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 TYR cc_start: 0.8245 (m-80) cc_final: 0.7793 (m-10) REVERT: L 32 ASN cc_start: 0.8634 (m-40) cc_final: 0.8421 (m-40) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.4637 time to fit residues: 30.0921 Evaluate side-chains 47 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** 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 = 0.3006 r_free = 0.3006 target = 0.040771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.030879 restraints weight = 73305.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.032751 restraints weight = 31935.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.033987 restraints weight = 17903.119| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3450 Z= 0.245 Angle : 0.584 6.248 4699 Z= 0.303 Chirality : 0.043 0.154 514 Planarity : 0.006 0.094 609 Dihedral : 5.917 53.811 511 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.41), residues: 421 helix: -1.89 (1.30), residues: 19 sheet: -0.33 (0.49), residues: 124 loop : -1.62 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.000 0.000 HIS A 519 PHE 0.011 0.001 PHE L 73 TYR 0.011 0.001 TYR A 495 ARG 0.011 0.001 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2379.58 seconds wall clock time: 42 minutes 56.80 seconds (2576.80 seconds total)