Starting phenix.real_space_refine on Tue Feb 13 04:45:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/02_2024/7ru8_24699.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/02_2024/7ru8_24699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/02_2024/7ru8_24699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/02_2024/7ru8_24699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/02_2024/7ru8_24699.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/02_2024/7ru8_24699.pdb" } resolution = 3.8 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= -0.001 sd= 0.014 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 15 5.16 5 C 2031 2.51 5 N 532 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3198 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 956 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "C" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1388 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 2 Chain: "A" 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 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.25, per 1000 atoms: 0.70 Number of scatterers: 3198 At special positions: 0 Unit cell: (56.65, 75.19, 107.12, 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 15 16.00 O 620 8.00 N 532 7.00 C 2031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 100D" distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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 A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN C 343 " " NAG L 201 " - " ASN L 28 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 584.3 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 742 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.494A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.550A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 100 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.826A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.584A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 108 hydrogen bonds defined for protein. 249 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: 0.89 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 623 1.32 - 1.45: 1156 1.45 - 1.59: 1469 1.59 - 1.73: 10 1.73 - 1.87: 17 Bond restraints: 3275 Sorted by residual: bond pdb=" CB LEU C 387 " pdb=" CG LEU C 387 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" CG PHE C 515 " pdb=" CD2 PHE C 515 " ideal model delta sigma weight residual 1.384 1.489 -0.105 2.10e-02 2.27e+03 2.51e+01 bond pdb=" CD ARG L 96 " pdb=" NE ARG L 96 " ideal model delta sigma weight residual 1.458 1.390 0.068 1.40e-02 5.10e+03 2.37e+01 bond pdb=" CG PHE C 515 " pdb=" CD1 PHE C 515 " ideal model delta sigma weight residual 1.384 1.486 -0.102 2.10e-02 2.27e+03 2.36e+01 bond pdb=" CG PHE C 429 " pdb=" CD2 PHE C 429 " ideal model delta sigma weight residual 1.384 1.486 -0.102 2.10e-02 2.27e+03 2.34e+01 ... (remaining 3270 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.66: 142 106.66 - 113.63: 1591 113.63 - 120.60: 1521 120.60 - 127.57: 1165 127.57 - 134.53: 24 Bond angle restraints: 4443 Sorted by residual: angle pdb=" N SER L 30 " pdb=" CA SER L 30 " pdb=" C SER L 30 " ideal model delta sigma weight residual 111.28 119.73 -8.45 1.09e+00 8.42e-01 6.01e+01 angle pdb=" C SER C 383 " pdb=" N PRO C 384 " pdb=" CA PRO C 384 " ideal model delta sigma weight residual 119.56 126.92 -7.36 1.01e+00 9.80e-01 5.31e+01 angle pdb=" N ARG H 94 " pdb=" CA ARG H 94 " pdb=" C ARG H 94 " ideal model delta sigma weight residual 113.17 122.27 -9.10 1.26e+00 6.30e-01 5.21e+01 angle pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta sigma weight residual 121.69 134.53 -12.84 1.85e+00 2.92e-01 4.82e+01 angle pdb=" N PRO H 41 " pdb=" CA PRO H 41 " pdb=" C PRO H 41 " ideal model delta sigma weight residual 111.26 100.42 10.84 1.63e+00 3.76e-01 4.42e+01 ... (remaining 4438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 1885 17.06 - 34.12: 53 34.12 - 51.19: 21 51.19 - 68.25: 7 68.25 - 85.31: 3 Dihedral angle restraints: 1969 sinusoidal: 799 harmonic: 1170 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 127.21 -34.21 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" N ILE H 31 " pdb=" C ILE H 31 " pdb=" CA ILE H 31 " pdb=" CB ILE H 31 " ideal model delta harmonic sigma weight residual 123.40 131.51 -8.11 0 2.50e+00 1.60e-01 1.05e+01 dihedral pdb=" C ARG L 96 " pdb=" N ARG L 96 " pdb=" CA ARG L 96 " pdb=" CB ARG L 96 " ideal model delta harmonic sigma weight residual -122.60 -114.72 -7.88 0 2.50e+00 1.60e-01 9.92e+00 ... (remaining 1966 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.103: 354 0.103 - 0.205: 97 0.205 - 0.307: 26 0.307 - 0.409: 4 0.409 - 0.511: 6 Chirality restraints: 487 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.51e+01 chirality pdb=" C1 NAG L 201 " pdb=" ND2 ASN L 28 " pdb=" C2 NAG L 201 " pdb=" O5 NAG L 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.91 0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" CG LEU C 387 " pdb=" CB LEU C 387 " pdb=" CD1 LEU C 387 " pdb=" CD2 LEU C 387 " both_signs ideal model delta sigma weight residual False -2.59 -3.09 0.51 2.00e-01 2.50e+01 6.38e+00 ... (remaining 484 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 28 " 0.061 2.00e-02 2.50e+03 6.58e-02 5.41e+01 pdb=" CG ASN L 28 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN L 28 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN L 28 " -0.105 2.00e-02 2.50e+03 pdb=" C1 NAG L 201 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 489 " 0.086 2.00e-02 2.50e+03 4.50e-02 4.04e+01 pdb=" CG TYR C 489 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 489 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR C 489 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 489 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR C 489 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR C 489 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 489 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.077 2.00e-02 2.50e+03 3.89e-02 3.79e+01 pdb=" CG TRP H 47 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.049 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 1160 2.86 - 3.37: 2899 3.37 - 3.88: 5523 3.88 - 4.39: 6414 4.39 - 4.90: 10245 Nonbonded interactions: 26241 Sorted by model distance: nonbonded pdb=" N VAL C 350 " pdb=" O VAL C 350 " model vdw 2.356 2.496 nonbonded pdb=" C SER C 349 " pdb=" O VAL C 350 " model vdw 2.474 3.270 nonbonded pdb=" N TYR H 32 " pdb=" O TYR H 32 " model vdw 2.478 2.496 nonbonded pdb=" N PHE C 429 " pdb=" O PHE C 429 " model vdw 2.504 2.496 nonbonded pdb=" N ALA H 40 " pdb=" O ALA H 40 " model vdw 2.504 2.496 ... (remaining 26236 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: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.980 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.830 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.022 0.125 3275 Z= 1.415 Angle : 1.867 12.843 4443 Z= 1.221 Chirality : 0.116 0.511 487 Planarity : 0.009 0.045 565 Dihedral : 10.389 85.311 1209 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.41), residues: 395 helix: -4.33 (0.37), residues: 21 sheet: 0.28 (0.44), residues: 134 loop : 0.10 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.017 TRP H 47 PHE 0.033 0.007 PHE C 429 TYR 0.086 0.009 TYR C 489 ARG 0.006 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.2506 (mttt) cc_final: 0.1758 (mtpp) REVERT: L 2 ILE cc_start: 0.7216 (mt) cc_final: 0.6844 (mt) REVERT: C 424 LYS cc_start: 0.8356 (tptt) cc_final: 0.7692 (tptt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2187 time to fit residues: 24.9650 Evaluate side-chains 49 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3275 Z= 0.271 Angle : 0.780 6.895 4443 Z= 0.418 Chirality : 0.047 0.150 487 Planarity : 0.004 0.029 565 Dihedral : 6.129 31.261 510 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.33 % Allowed : 12.50 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.43), residues: 395 helix: -3.50 (0.79), residues: 21 sheet: 0.18 (0.49), residues: 129 loop : -0.27 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 47 PHE 0.031 0.002 PHE L 71 TYR 0.024 0.002 TYR L 87 ARG 0.004 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.8453 (tp40) cc_final: 0.8251 (tp40) REVERT: H 13 LYS cc_start: 0.2582 (mttt) cc_final: 0.1994 (tttm) REVERT: L 38 GLN cc_start: 0.7802 (tt0) cc_final: 0.7552 (tm-30) REVERT: C 353 TRP cc_start: 0.6439 (m-90) cc_final: 0.6122 (m-90) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.1717 time to fit residues: 12.8253 Evaluate side-chains 52 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.0170 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3275 Z= 0.267 Angle : 0.717 6.304 4443 Z= 0.386 Chirality : 0.047 0.226 487 Planarity : 0.004 0.025 565 Dihedral : 6.603 35.765 510 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.91 % Allowed : 12.79 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.42), residues: 395 helix: -3.00 (1.25), residues: 14 sheet: 0.14 (0.50), residues: 130 loop : -0.73 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 47 PHE 0.025 0.003 PHE C 429 TYR 0.020 0.002 TYR C 489 ARG 0.005 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.7091 (t60) cc_final: 0.6863 (t60) REVERT: L 103 LYS cc_start: 0.7745 (tptm) cc_final: 0.7306 (tppt) REVERT: C 353 TRP cc_start: 0.6577 (m-90) cc_final: 0.6365 (m-90) REVERT: C 387 LEU cc_start: 0.8212 (tp) cc_final: 0.7802 (tp) outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.1622 time to fit residues: 11.8651 Evaluate side-chains 53 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 23 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3275 Z= 0.253 Angle : 0.689 6.277 4443 Z= 0.367 Chirality : 0.047 0.208 487 Planarity : 0.004 0.038 565 Dihedral : 6.985 43.508 510 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.78 % Allowed : 14.24 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.03 (0.42), residues: 395 helix: -2.73 (1.29), residues: 15 sheet: -0.12 (0.49), residues: 132 loop : -0.86 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 PHE 0.022 0.002 PHE L 71 TYR 0.013 0.002 TYR C 489 ARG 0.002 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 103 LYS cc_start: 0.7525 (tptm) cc_final: 0.6930 (tptt) REVERT: C 387 LEU cc_start: 0.8258 (tp) cc_final: 0.7915 (tp) outliers start: 13 outliers final: 10 residues processed: 56 average time/residue: 0.1729 time to fit residues: 11.7185 Evaluate side-chains 53 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.0050 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3275 Z= 0.270 Angle : 0.684 6.070 4443 Z= 0.368 Chirality : 0.046 0.212 487 Planarity : 0.004 0.038 565 Dihedral : 7.214 47.218 510 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.65 % Allowed : 13.66 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.19 (0.43), residues: 395 helix: -2.74 (1.07), residues: 22 sheet: -0.07 (0.50), residues: 128 loop : -1.00 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 353 PHE 0.016 0.002 PHE L 71 TYR 0.012 0.002 TYR L 49 ARG 0.006 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8358 (tmmt) REVERT: L 74 THR cc_start: 0.4378 (OUTLIER) cc_final: 0.3935 (p) REVERT: L 103 LYS cc_start: 0.7308 (tptm) cc_final: 0.6848 (tptt) REVERT: C 387 LEU cc_start: 0.8405 (tp) cc_final: 0.8071 (tp) outliers start: 16 outliers final: 12 residues processed: 52 average time/residue: 0.1881 time to fit residues: 11.8707 Evaluate side-chains 53 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3275 Z= 0.304 Angle : 0.703 6.041 4443 Z= 0.377 Chirality : 0.046 0.214 487 Planarity : 0.005 0.037 565 Dihedral : 7.535 50.998 510 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 5.52 % Allowed : 13.66 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.36 (0.43), residues: 395 helix: -3.13 (0.89), residues: 28 sheet: 0.12 (0.51), residues: 119 loop : -1.18 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP C 353 PHE 0.015 0.002 PHE L 71 TYR 0.016 0.002 TYR C 351 ARG 0.006 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 40 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8312 (tmmt) REVERT: L 74 THR cc_start: 0.4664 (OUTLIER) cc_final: 0.4257 (p) REVERT: C 387 LEU cc_start: 0.8454 (tp) cc_final: 0.8153 (tp) REVERT: C 466 ARG cc_start: 0.5936 (mpt90) cc_final: 0.5028 (ttt-90) outliers start: 19 outliers final: 13 residues processed: 52 average time/residue: 0.1782 time to fit residues: 11.2173 Evaluate side-chains 52 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 37 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 22 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3275 Z= 0.200 Angle : 0.619 5.989 4443 Z= 0.332 Chirality : 0.045 0.198 487 Planarity : 0.004 0.037 565 Dihedral : 6.911 47.423 510 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 4.07 % Allowed : 15.41 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.32 (0.43), residues: 395 helix: -3.22 (0.87), residues: 28 sheet: 0.08 (0.53), residues: 114 loop : -1.08 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP C 353 PHE 0.011 0.001 PHE C 429 TYR 0.015 0.001 TYR C 351 ARG 0.009 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: L 74 THR cc_start: 0.4247 (OUTLIER) cc_final: 0.3944 (p) REVERT: L 103 LYS cc_start: 0.6910 (tptm) cc_final: 0.6407 (tppt) REVERT: C 365 TYR cc_start: 0.5904 (m-80) cc_final: 0.5651 (m-80) REVERT: C 387 LEU cc_start: 0.8342 (tp) cc_final: 0.7966 (tp) outliers start: 14 outliers final: 11 residues processed: 51 average time/residue: 0.1861 time to fit residues: 11.4389 Evaluate side-chains 51 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3275 Z= 0.206 Angle : 0.613 5.939 4443 Z= 0.328 Chirality : 0.045 0.191 487 Planarity : 0.004 0.037 565 Dihedral : 6.742 45.084 510 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.65 % Allowed : 15.41 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.31 (0.43), residues: 395 helix: -3.29 (0.84), residues: 28 sheet: 0.09 (0.53), residues: 114 loop : -1.06 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 353 PHE 0.011 0.001 PHE C 429 TYR 0.015 0.001 TYR C 351 ARG 0.002 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: L 74 THR cc_start: 0.4398 (OUTLIER) cc_final: 0.4003 (p) REVERT: L 103 LYS cc_start: 0.6838 (tptm) cc_final: 0.6060 (tppt) outliers start: 16 outliers final: 12 residues processed: 47 average time/residue: 0.1290 time to fit residues: 7.7059 Evaluate side-chains 50 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.0170 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3275 Z= 0.174 Angle : 0.617 11.043 4443 Z= 0.321 Chirality : 0.045 0.184 487 Planarity : 0.004 0.038 565 Dihedral : 6.431 42.864 510 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.20 % Allowed : 16.57 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.43), residues: 395 helix: -3.31 (0.81), residues: 28 sheet: 0.12 (0.53), residues: 114 loop : -1.01 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 353 PHE 0.012 0.001 PHE C 429 TYR 0.015 0.001 TYR C 351 ARG 0.002 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: L 74 THR cc_start: 0.4242 (OUTLIER) cc_final: 0.3873 (p) outliers start: 11 outliers final: 10 residues processed: 49 average time/residue: 0.1544 time to fit residues: 9.6404 Evaluate side-chains 46 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3275 Z= 0.227 Angle : 0.647 9.624 4443 Z= 0.337 Chirality : 0.047 0.195 487 Planarity : 0.004 0.037 565 Dihedral : 6.777 44.853 510 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.20 % Allowed : 17.15 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.32 (0.43), residues: 395 helix: -3.34 (0.80), residues: 28 sheet: 0.11 (0.54), residues: 114 loop : -1.08 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 353 PHE 0.011 0.001 PHE C 429 TYR 0.016 0.001 TYR C 351 ARG 0.002 0.000 ARG C 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: L 74 THR cc_start: 0.4406 (OUTLIER) cc_final: 0.4080 (p) REVERT: L 103 LYS cc_start: 0.6807 (tptm) cc_final: 0.6066 (tppt) outliers start: 11 outliers final: 9 residues processed: 39 average time/residue: 0.1678 time to fit residues: 8.0249 Evaluate side-chains 40 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.0010 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 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 = 0.3717 r_free = 0.3717 target = 0.078170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.071689 restraints weight = 14368.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.073222 restraints weight = 7559.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.074174 restraints weight = 4605.734| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3275 Z= 0.199 Angle : 0.642 8.572 4443 Z= 0.334 Chirality : 0.046 0.188 487 Planarity : 0.004 0.036 565 Dihedral : 6.641 44.811 510 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.78 % Allowed : 17.44 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.35 (0.43), residues: 395 helix: -3.33 (0.82), residues: 28 sheet: 0.04 (0.54), residues: 114 loop : -1.07 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 353 PHE 0.011 0.001 PHE C 429 TYR 0.010 0.001 TYR C 489 ARG 0.002 0.000 ARG C 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1333.70 seconds wall clock time: 24 minutes 47.58 seconds (1487.58 seconds total)