Starting phenix.real_space_refine on Thu Dec 7 18:19:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/12_2023/7swp_25478_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/12_2023/7swp_25478.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/7swp_25478/12_2023/7swp_25478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/12_2023/7swp_25478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/12_2023/7swp_25478_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/12_2023/7swp_25478_neut.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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2137 2.51 5 N 573 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 34": "OD1" <-> "OD2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "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: 3372 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1545 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1017 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 810 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.30, per 1000 atoms: 0.68 Number of scatterers: 3372 At special positions: 0 Unit cell: (84.15, 59.4, 89.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 648 8.00 N 573 7.00 C 2137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 605.5 milliseconds 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 15.1% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.584A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.236A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.828A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.876A pdb=" N TYR H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.782A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.547A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.687A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.623A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 23 119 hydrogen bonds defined for protein. 273 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: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1087 1.34 - 1.46: 924 1.46 - 1.58: 1434 1.58 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3461 Sorted by residual: bond pdb=" C TYR A 421 " pdb=" N ASN A 422 " ideal model delta sigma weight residual 1.332 1.282 0.050 1.40e-02 5.10e+03 1.27e+01 bond pdb=" C LYS A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 1.331 1.233 0.098 2.83e-02 1.25e+03 1.19e+01 bond pdb=" N VAL L 100 " pdb=" CA VAL L 100 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.21e-02 6.83e+03 8.88e+00 bond pdb=" N VAL L 101 " pdb=" CA VAL L 101 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.24e-02 6.50e+03 8.21e+00 bond pdb=" N THR L 106 " pdb=" CA THR L 106 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.96e+00 ... (remaining 3456 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.86: 113 106.86 - 113.65: 1798 113.65 - 120.43: 1310 120.43 - 127.21: 1450 127.21 - 133.99: 36 Bond angle restraints: 4707 Sorted by residual: angle pdb=" C HIS L 36 " pdb=" N TRP L 37 " pdb=" CA TRP L 37 " ideal model delta sigma weight residual 122.94 115.73 7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" C TYR A 421 " pdb=" N ASN A 422 " pdb=" CA ASN A 422 " ideal model delta sigma weight residual 121.54 113.51 8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C PRO A 527 " pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 121.70 127.24 -5.54 1.80e+00 3.09e-01 9.48e+00 angle pdb=" N GLY A 526 " pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 112.34 118.59 -6.25 2.04e+00 2.40e-01 9.38e+00 angle pdb=" CA GLY L 103 " pdb=" C GLY L 103 " pdb=" O GLY L 103 " ideal model delta sigma weight residual 122.24 118.32 3.92 1.30e+00 5.92e-01 9.10e+00 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1840 17.57 - 35.15: 163 35.15 - 52.72: 15 52.72 - 70.29: 4 70.29 - 87.87: 2 Dihedral angle restraints: 2024 sinusoidal: 776 harmonic: 1248 Sorted by residual: dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.90 46.10 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CA SER A 477 " pdb=" C SER A 477 " pdb=" N THR A 478 " pdb=" CA THR A 478 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 2021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 354 0.048 - 0.096: 103 0.096 - 0.145: 33 0.145 - 0.193: 3 0.193 - 0.241: 2 Chirality restraints: 495 Sorted by residual: chirality pdb=" CB ILE L 50 " pdb=" CA ILE L 50 " pdb=" CG1 ILE L 50 " pdb=" CG2 ILE L 50 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU H 81 " pdb=" CB LEU H 81 " pdb=" CD1 LEU H 81 " pdb=" CD2 LEU H 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL L 101 " pdb=" N VAL L 101 " pdb=" C VAL L 101 " pdb=" CB VAL L 101 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 492 not shown) Planarity restraints: 617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 37 " -0.035 2.00e-02 2.50e+03 4.40e-02 4.85e+01 pdb=" CG TRP L 37 " 0.109 2.00e-02 2.50e+03 pdb=" CD1 TRP L 37 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP L 37 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP L 37 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP L 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP L 37 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 37 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 37 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP L 37 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 527 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 453 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C TYR A 453 " -0.025 2.00e-02 2.50e+03 pdb=" O TYR A 453 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG A 454 " 0.009 2.00e-02 2.50e+03 ... (remaining 614 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 569 2.74 - 3.28: 3775 3.28 - 3.82: 6048 3.82 - 4.36: 7001 4.36 - 4.90: 11348 Nonbonded interactions: 28741 Sorted by model distance: nonbonded pdb=" OD2 ASP L 94 " pdb=" OG SER L 96 " model vdw 2.202 2.440 nonbonded pdb=" NE2 GLN H 13 " pdb=" O SER H 128 " model vdw 2.206 2.520 nonbonded pdb=" O TYR H 53 " pdb=" NH2 ARG H 72 " model vdw 2.214 2.520 nonbonded pdb=" OG1 THR A 415 " pdb=" OG SER L 58 " model vdw 2.216 2.440 nonbonded pdb=" O LYS A 444 " pdb=" NE2 GLN A 498 " model vdw 2.224 2.520 ... (remaining 28736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.000 Extract box with map and model: 3.000 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.050 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.008 0.098 3461 Z= 0.534 Angle : 0.925 8.029 4707 Z= 0.525 Chirality : 0.051 0.241 495 Planarity : 0.006 0.056 617 Dihedral : 12.869 87.868 1224 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 40.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.38), residues: 430 helix: -3.11 (0.87), residues: 21 sheet: -1.11 (0.44), residues: 122 loop : -1.50 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.006 TRP L 37 HIS 0.007 0.003 HIS L 36 PHE 0.023 0.002 PHE A 490 TYR 0.021 0.003 TYR L 51 ARG 0.011 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1936 time to fit residues: 36.1603 Evaluate side-chains 93 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3461 Z= 0.248 Angle : 0.782 9.158 4707 Z= 0.400 Chirality : 0.049 0.135 495 Planarity : 0.006 0.042 617 Dihedral : 5.814 24.894 487 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.57 % Allowed : 14.56 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.37), residues: 430 helix: -3.37 (0.72), residues: 22 sheet: -0.91 (0.42), residues: 132 loop : -1.21 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP L 37 HIS 0.007 0.003 HIS A 519 PHE 0.018 0.003 PHE A 392 TYR 0.023 0.002 TYR A 365 ARG 0.008 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 123 average time/residue: 0.1498 time to fit residues: 22.5671 Evaluate side-chains 106 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0431 time to fit residues: 1.0224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.0020 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3461 Z= 0.251 Angle : 0.726 6.762 4707 Z= 0.379 Chirality : 0.047 0.141 495 Planarity : 0.005 0.045 617 Dihedral : 5.363 25.189 487 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.40 % Allowed : 19.23 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.38), residues: 430 helix: -3.48 (0.69), residues: 22 sheet: -0.65 (0.42), residues: 132 loop : -0.98 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP L 37 HIS 0.006 0.003 HIS L 36 PHE 0.021 0.002 PHE A 392 TYR 0.029 0.002 TYR A 351 ARG 0.005 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 113 average time/residue: 0.1282 time to fit residues: 18.1038 Evaluate side-chains 115 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0383 time to fit residues: 1.4081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3461 Z= 0.395 Angle : 0.800 9.045 4707 Z= 0.425 Chirality : 0.049 0.154 495 Planarity : 0.006 0.058 617 Dihedral : 5.836 26.074 487 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.67 % Allowed : 20.88 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.38), residues: 430 helix: -3.63 (0.69), residues: 22 sheet: -0.76 (0.43), residues: 123 loop : -1.07 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP L 37 HIS 0.006 0.002 HIS H 118 PHE 0.020 0.003 PHE A 392 TYR 0.026 0.003 TYR A 365 ARG 0.007 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 0.1339 time to fit residues: 19.7341 Evaluate side-chains 108 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0315 time to fit residues: 1.0326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0270 chunk 16 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3461 Z= 0.213 Angle : 0.743 10.852 4707 Z= 0.380 Chirality : 0.047 0.163 495 Planarity : 0.005 0.040 617 Dihedral : 5.178 22.420 487 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.47 % Allowed : 23.90 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.39), residues: 430 helix: -3.56 (0.70), residues: 22 sheet: -0.41 (0.44), residues: 132 loop : -0.89 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 37 HIS 0.005 0.002 HIS L 36 PHE 0.016 0.002 PHE A 392 TYR 0.023 0.002 TYR A 365 ARG 0.003 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 118 average time/residue: 0.1445 time to fit residues: 20.9567 Evaluate side-chains 111 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0458 time to fit residues: 1.1089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3461 Z= 0.198 Angle : 0.740 11.318 4707 Z= 0.377 Chirality : 0.047 0.173 495 Planarity : 0.005 0.042 617 Dihedral : 4.980 21.562 487 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.75 % Allowed : 25.00 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.40), residues: 430 helix: -3.88 (0.59), residues: 22 sheet: -0.27 (0.44), residues: 131 loop : -0.92 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 37 HIS 0.013 0.004 HIS L 36 PHE 0.018 0.002 PHE A 392 TYR 0.022 0.001 TYR A 365 ARG 0.003 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 117 average time/residue: 0.1446 time to fit residues: 20.7895 Evaluate side-chains 116 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0391 time to fit residues: 1.1505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 3461 Z= 0.468 Angle : 0.821 10.155 4707 Z= 0.440 Chirality : 0.051 0.174 495 Planarity : 0.007 0.063 617 Dihedral : 5.846 20.640 487 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 32.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.85 % Allowed : 25.82 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.39), residues: 430 helix: -3.52 (0.60), residues: 28 sheet: -0.47 (0.44), residues: 135 loop : -1.17 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 37 HIS 0.013 0.005 HIS L 36 PHE 0.022 0.003 PHE A 392 TYR 0.022 0.003 TYR H 115 ARG 0.006 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 112 average time/residue: 0.1248 time to fit residues: 17.4069 Evaluate side-chains 111 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0369 time to fit residues: 1.2388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3461 Z= 0.207 Angle : 0.745 10.024 4707 Z= 0.380 Chirality : 0.048 0.179 495 Planarity : 0.006 0.047 617 Dihedral : 5.128 21.240 487 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.20 % Allowed : 25.82 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.39), residues: 430 helix: -3.67 (0.62), residues: 28 sheet: -0.30 (0.46), residues: 123 loop : -1.04 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.012 0.003 HIS L 36 PHE 0.019 0.002 PHE A 392 TYR 0.024 0.002 TYR H 115 ARG 0.004 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 114 average time/residue: 0.1504 time to fit residues: 21.1085 Evaluate side-chains 108 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0426 time to fit residues: 1.0462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3461 Z= 0.261 Angle : 0.805 13.586 4707 Z= 0.410 Chirality : 0.049 0.173 495 Planarity : 0.006 0.047 617 Dihedral : 5.065 21.533 487 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.92 % Allowed : 30.22 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.40), residues: 430 helix: -3.70 (0.63), residues: 28 sheet: -0.10 (0.46), residues: 131 loop : -1.13 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 47 HIS 0.010 0.003 HIS L 36 PHE 0.020 0.002 PHE A 392 TYR 0.028 0.002 TYR H 115 ARG 0.005 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 106 average time/residue: 0.1423 time to fit residues: 18.5316 Evaluate side-chains 107 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0417 time to fit residues: 0.9822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2002 > 50: distance: 6 - 8: 23.462 distance: 8 - 9: 19.083 distance: 8 - 136: 26.388 distance: 9 - 10: 41.835 distance: 10 - 11: 20.099 distance: 10 - 12: 33.058 distance: 11 - 146: 8.262 distance: 12 - 13: 18.382 distance: 13 - 14: 12.710 distance: 13 - 16: 8.520 distance: 14 - 15: 11.027 distance: 14 - 19: 23.000 distance: 16 - 17: 21.005 distance: 16 - 18: 19.100 distance: 19 - 20: 12.092 distance: 19 - 149: 15.243 distance: 20 - 21: 16.235 distance: 20 - 23: 12.270 distance: 21 - 22: 16.744 distance: 21 - 26: 5.021 distance: 23 - 24: 13.191 distance: 23 - 25: 22.958 distance: 26 - 27: 17.967 distance: 27 - 28: 32.361 distance: 27 - 30: 23.964 distance: 28 - 29: 11.339 distance: 28 - 35: 17.563 distance: 30 - 31: 20.961 distance: 31 - 32: 10.518 distance: 32 - 33: 14.737 distance: 32 - 34: 30.310 distance: 35 - 36: 22.729 distance: 35 - 41: 7.943 distance: 36 - 37: 24.443 distance: 36 - 39: 21.278 distance: 37 - 38: 31.269 distance: 37 - 42: 10.777 distance: 39 - 40: 38.994 distance: 40 - 41: 50.200 distance: 42 - 43: 10.518 distance: 43 - 44: 27.130 distance: 44 - 45: 25.414 distance: 44 - 46: 49.012 distance: 46 - 47: 16.419 distance: 47 - 48: 20.443 distance: 47 - 50: 17.241 distance: 48 - 49: 20.062 distance: 48 - 57: 35.737 distance: 50 - 51: 21.134 distance: 51 - 52: 28.994 distance: 52 - 53: 13.161 distance: 53 - 54: 7.731 distance: 54 - 55: 18.755 distance: 54 - 56: 6.051 distance: 57 - 58: 24.387 distance: 58 - 59: 20.758 distance: 58 - 61: 17.309 distance: 59 - 60: 10.390 distance: 59 - 63: 13.179 distance: 61 - 62: 32.653 distance: 63 - 64: 20.040 distance: 63 - 113: 12.581 distance: 64 - 65: 12.238 distance: 64 - 67: 11.087 distance: 65 - 66: 7.688 distance: 65 - 71: 11.807 distance: 66 - 110: 11.671 distance: 67 - 68: 13.516 distance: 68 - 69: 20.309 distance: 68 - 70: 22.049 distance: 71 - 72: 7.112 distance: 72 - 73: 6.062 distance: 72 - 75: 3.673 distance: 73 - 74: 5.237 distance: 73 - 82: 4.516 distance: 75 - 76: 13.089 distance: 76 - 77: 4.502 distance: 77 - 78: 7.220 distance: 79 - 80: 5.969 distance: 79 - 81: 3.151