Starting phenix.real_space_refine on Thu Dec 7 17:25:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/12_2023/7ru8_24699.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/12_2023/7ru8_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_24699/12_2023/7ru8_24699.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/12_2023/7ru8_24699.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/12_2023/7ru8_24699.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru8_24699/12_2023/7ru8_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-1.21rc1-5172/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: 1.29 Conformation dependent library (CDL) restraints added in 562.1 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: 0.36 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: 0.82 Time building geometry restraints manager: 1.39 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: 3.850 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: 18.030 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.480 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.380 ------------------------------------------------------------------------------- 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 : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2193 time to fit residues: 24.9660 Evaluate side-chains 48 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5078 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 0.6980 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: 0.8980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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: 0.7338 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3275 Z= 0.263 Angle : 0.772 6.655 4443 Z= 0.414 Chirality : 0.048 0.161 487 Planarity : 0.005 0.027 565 Dihedral : 6.183 31.749 510 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.62 % Allowed : 12.79 % Favored : 84.59 % 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: -0.58 (0.43), residues: 395 helix: -2.88 (0.96), residues: 21 sheet: -0.06 (0.46), residues: 145 loop : -0.26 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP H 47 PHE 0.030 0.002 PHE L 71 TYR 0.026 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: 9 poor density : 59 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.1703 time to fit residues: 12.6482 Evaluate side-chains 48 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0422 time to fit residues: 0.8380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN C 481 ASN C 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3275 Z= 0.278 Angle : 0.729 6.272 4443 Z= 0.391 Chirality : 0.047 0.210 487 Planarity : 0.004 0.029 565 Dihedral : 6.675 36.259 510 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.33 % Allowed : 11.92 % Favored : 85.76 % 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: -0.89 (0.42), residues: 395 helix: -3.23 (1.10), residues: 14 sheet: 0.17 (0.50), residues: 130 loop : -0.85 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 353 PHE 0.025 0.003 PHE L 71 TYR 0.020 0.002 TYR C 489 ARG 0.006 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 61 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.1689 time to fit residues: 12.0508 Evaluate side-chains 48 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0341 time to fit residues: 0.7511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.0010 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3275 Z= 0.228 Angle : 0.652 6.303 4443 Z= 0.350 Chirality : 0.045 0.127 487 Planarity : 0.004 0.031 565 Dihedral : 6.712 40.671 510 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.62 % Allowed : 13.37 % Favored : 84.01 % 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: -1.02 (0.42), residues: 395 helix: -2.76 (1.26), residues: 15 sheet: -0.03 (0.49), residues: 132 loop : -0.90 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 353 PHE 0.027 0.002 PHE L 71 TYR 0.015 0.001 TYR C 489 ARG 0.005 0.001 ARG C 466 *********************** 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 60 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 0.1709 time to fit residues: 11.3987 Evaluate side-chains 50 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0457 time to fit residues: 0.8541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3275 Z= 0.211 Angle : 0.624 6.068 4443 Z= 0.337 Chirality : 0.044 0.130 487 Planarity : 0.004 0.048 565 Dihedral : 6.612 41.558 510 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.03 % Allowed : 15.12 % Favored : 82.85 % 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: -0.88 (0.43), residues: 395 helix: -2.75 (1.27), residues: 15 sheet: 0.17 (0.50), residues: 130 loop : -0.86 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP C 353 PHE 0.019 0.002 PHE L 71 TYR 0.012 0.001 TYR C 489 ARG 0.011 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: 7 poor density : 52 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 57 average time/residue: 0.1949 time to fit residues: 13.1787 Evaluate side-chains 46 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1252 time to fit residues: 0.9365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5945 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= 0.229 Angle : 0.642 9.421 4443 Z= 0.342 Chirality : 0.044 0.159 487 Planarity : 0.004 0.047 565 Dihedral : 6.670 43.287 510 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.33 % Allowed : 14.83 % Favored : 82.85 % 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: -0.85 (0.43), residues: 395 helix: -2.96 (1.00), residues: 22 sheet: 0.41 (0.52), residues: 123 loop : -0.86 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 47 PHE 0.012 0.001 PHE C 429 TYR 0.010 0.001 TYR C 489 ARG 0.007 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 51 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.1693 time to fit residues: 9.4849 Evaluate side-chains 46 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0426 time to fit residues: 0.9943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 22 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3275 Z= 0.201 Angle : 0.624 8.578 4443 Z= 0.329 Chirality : 0.044 0.145 487 Planarity : 0.004 0.046 565 Dihedral : 6.509 43.407 510 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 1.45 % Allowed : 15.99 % Favored : 82.56 % 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: -0.92 (0.43), residues: 395 helix: -3.27 (0.87), residues: 22 sheet: 0.67 (0.54), residues: 113 loop : -1.00 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 PHE 0.012 0.001 PHE C 429 TYR 0.010 0.001 TYR C 489 ARG 0.006 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 44 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.1517 time to fit residues: 7.7959 Evaluate side-chains 40 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0347 time to fit residues: 0.6021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3275 Z= 0.186 Angle : 0.609 6.712 4443 Z= 0.326 Chirality : 0.044 0.135 487 Planarity : 0.004 0.049 565 Dihedral : 6.371 42.100 510 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.16 % Allowed : 15.99 % Favored : 82.85 % 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: -1.02 (0.43), residues: 395 helix: -3.44 (0.75), residues: 28 sheet: 0.63 (0.55), residues: 111 loop : -0.99 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 47 PHE 0.010 0.001 PHE C 429 TYR 0.010 0.001 TYR C 365 ARG 0.005 0.000 ARG C 466 *********************** 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 46 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.1497 time to fit residues: 8.3530 Evaluate side-chains 40 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0425 time to fit residues: 0.6833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 chunk 17 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.0570 chunk 35 optimal weight: 0.0270 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3275 Z= 0.156 Angle : 0.627 10.639 4443 Z= 0.321 Chirality : 0.045 0.143 487 Planarity : 0.004 0.048 565 Dihedral : 5.872 37.864 510 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.87 % Allowed : 17.44 % 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: -0.95 (0.44), residues: 395 helix: -3.49 (0.74), residues: 28 sheet: 0.66 (0.55), residues: 111 loop : -0.91 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 47 PHE 0.010 0.001 PHE C 429 TYR 0.009 0.001 TYR C 489 ARG 0.006 0.000 ARG C 466 *********************** 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 46 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 0.1753 time to fit residues: 9.4994 Evaluate side-chains 38 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0345 time to fit residues: 0.6080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.6712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3275 Z= 0.240 Angle : 0.689 11.715 4443 Z= 0.358 Chirality : 0.045 0.141 487 Planarity : 0.004 0.046 565 Dihedral : 6.505 41.058 510 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.87 % Allowed : 17.73 % Favored : 81.40 % 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: -1.22 (0.42), residues: 395 helix: -3.47 (0.73), residues: 28 sheet: 0.76 (0.55), residues: 104 loop : -1.23 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 PHE 0.010 0.001 PHE C 338 TYR 0.011 0.001 TYR C 365 ARG 0.007 0.001 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 43 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.1942 time to fit residues: 10.2661 Evaluate side-chains 39 residues out of total 344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0471 time to fit residues: 0.8685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.0060 chunk 35 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3772 r_free = 0.3772 target = 0.080614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.074358 restraints weight = 14749.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.075843 restraints weight = 7916.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.076787 restraints weight = 4865.681| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3275 Z= 0.180 Angle : 0.650 12.006 4443 Z= 0.329 Chirality : 0.045 0.145 487 Planarity : 0.004 0.047 565 Dihedral : 6.144 39.458 510 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 19.19 % 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: -1.19 (0.42), residues: 395 helix: -3.35 (0.77), residues: 28 sheet: 0.53 (0.54), residues: 106 loop : -1.11 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 47 PHE 0.010 0.001 PHE C 429 TYR 0.010 0.001 TYR C 396 ARG 0.006 0.000 ARG C 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1360.66 seconds wall clock time: 25 minutes 18.26 seconds (1518.26 seconds total)