Starting phenix.real_space_refine on Sun Mar 10 19:37:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj0_25149/03_2024/7sj0_25149.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj0_25149/03_2024/7sj0_25149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj0_25149/03_2024/7sj0_25149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj0_25149/03_2024/7sj0_25149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj0_25149/03_2024/7sj0_25149.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj0_25149/03_2024/7sj0_25149.pdb" } resolution = 3.36 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 812 atoms to isotropic. 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 2279 2.51 5 N 593 2.21 5 O 704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3590 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1806 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain breaks: 4 Chain: "B" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 784 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.49, per 1000 atoms: 0.69 Number of scatterers: 3590 At special positions: 0 Unit cell: (99, 78.1, 94.6, 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 704 8.00 N 593 7.00 C 2279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 17 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 149 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 776.7 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 9 sheets defined 2.0% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'B' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.312A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 4.045A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A 69 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.702A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 155 removed outlier: 4.000A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.735A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.846A pdb=" N THR B 119 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 92 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 99 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.525A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 46 through 50 removed outlier: 3.640A pdb=" N GLN L 38 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER L 35 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY L 90 " --> pdb=" O SER L 35 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 228 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: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1130 1.34 - 1.46: 942 1.46 - 1.58: 1584 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3676 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 3671 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.06: 118 107.06 - 113.82: 2009 113.82 - 120.57: 1273 120.57 - 127.32: 1553 127.32 - 134.07: 43 Bond angle restraints: 4996 Sorted by residual: angle pdb=" CA THR A 33 " pdb=" CB THR A 33 " pdb=" CG2 THR A 33 " ideal model delta sigma weight residual 110.50 114.45 -3.95 1.70e+00 3.46e-01 5.39e+00 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 119.53 -5.13 2.30e+00 1.89e-01 4.98e+00 angle pdb=" CA LEU L 96 " pdb=" CB LEU L 96 " pdb=" CG LEU L 96 " ideal model delta sigma weight residual 116.30 123.84 -7.54 3.50e+00 8.16e-02 4.65e+00 angle pdb=" CB MET B 34 " pdb=" CG MET B 34 " pdb=" SD MET B 34 " ideal model delta sigma weight residual 112.70 118.84 -6.14 3.00e+00 1.11e-01 4.20e+00 angle pdb=" C PHE A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 122.68 125.62 -2.94 1.47e+00 4.63e-01 4.01e+00 ... (remaining 4991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 2034 17.30 - 34.60: 135 34.60 - 51.90: 33 51.90 - 69.20: 8 69.20 - 86.49: 3 Dihedral angle restraints: 2213 sinusoidal: 922 harmonic: 1291 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -135.37 49.37 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CA ASN A 99 " pdb=" C ASN A 99 " pdb=" N ILE A 100 " pdb=" CA ILE A 100 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA THR A 167 " pdb=" C THR A 167 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 2210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 503 0.082 - 0.164: 60 0.164 - 0.246: 0 0.246 - 0.328: 1 0.328 - 0.410: 1 Chirality restraints: 565 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 562 not shown) Planarity restraints: 637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 55 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO L 56 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO L 56 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO L 56 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 99 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C ASN A 99 " 0.021 2.00e-02 2.50e+03 pdb=" O ASN A 99 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 100 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.010 2.00e-02 2.50e+03 9.87e-03 1.22e+00 pdb=" CG ASN A 61 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.011 2.00e-02 2.50e+03 ... (remaining 634 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 512 2.76 - 3.30: 3344 3.30 - 3.83: 4986 3.83 - 4.37: 5454 4.37 - 4.90: 10160 Nonbonded interactions: 24456 Sorted by model distance: nonbonded pdb=" OG SER L 68 " pdb=" OG SER L 71 " model vdw 2.225 2.440 nonbonded pdb=" O GLY L 30 " pdb=" NZ LYS L 67 " model vdw 2.273 2.520 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.300 2.440 nonbonded pdb=" NZ LYS A 129 " pdb=" O PHE A 168 " model vdw 2.337 2.520 nonbonded pdb=" OG1 THR A 124 " pdb=" O7 NAG A1301 " model vdw 2.337 2.440 ... (remaining 24451 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 15.520 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 14.230 Find NCS groups from input model: 0.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3676 Z= 0.209 Angle : 0.656 7.544 4996 Z= 0.331 Chirality : 0.052 0.410 565 Planarity : 0.004 0.030 632 Dihedral : 12.810 86.494 1377 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.98 (0.38), residues: 438 helix: None (None), residues: 0 sheet: -0.01 (0.42), residues: 141 loop : -2.13 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 108 HIS 0.001 0.000 HIS A 69 PHE 0.012 0.001 PHE A 238 TYR 0.010 0.001 TYR B 27 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.407 Fit side-chains REVERT: A 69 HIS cc_start: 0.7608 (t-90) cc_final: 0.7232 (t-90) REVERT: A 128 ILE cc_start: 0.8539 (mp) cc_final: 0.8327 (mp) REVERT: A 144 TYR cc_start: 0.8296 (p90) cc_final: 0.8091 (p90) REVERT: A 202 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8367 (mtpt) REVERT: B 64 PHE cc_start: 0.8333 (m-10) cc_final: 0.8057 (m-10) REVERT: B 107 ASN cc_start: 0.7869 (p0) cc_final: 0.7609 (p0) REVERT: L 76 ILE cc_start: 0.8006 (tp) cc_final: 0.7749 (tt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1755 time to fit residues: 22.3735 Evaluate side-chains 94 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.0370 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3676 Z= 0.291 Angle : 0.697 8.577 4996 Z= 0.364 Chirality : 0.055 0.538 565 Planarity : 0.005 0.032 632 Dihedral : 7.642 59.152 587 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.31 % Allowed : 12.34 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.71 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.50 (0.43), residues: 144 loop : -2.17 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 108 HIS 0.003 0.001 HIS B 35 PHE 0.016 0.002 PHE A 86 TYR 0.016 0.002 TYR B 27 ARG 0.008 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.405 Fit side-chains REVERT: A 128 ILE cc_start: 0.8579 (mp) cc_final: 0.8306 (mp) REVERT: A 202 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8299 (mtpt) REVERT: B 107 ASN cc_start: 0.7960 (p0) cc_final: 0.7630 (p0) REVERT: L 55 ARG cc_start: 0.7317 (ptm160) cc_final: 0.7031 (ptm160) outliers start: 9 outliers final: 4 residues processed: 99 average time/residue: 0.1851 time to fit residues: 21.8936 Evaluate side-chains 96 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 0.0670 chunk 11 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3676 Z= 0.238 Angle : 0.653 7.846 4996 Z= 0.340 Chirality : 0.052 0.485 565 Planarity : 0.005 0.036 632 Dihedral : 7.260 58.952 587 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.57 % Allowed : 14.91 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.53 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.51 (0.40), residues: 159 loop : -2.10 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 104 HIS 0.002 0.000 HIS B 35 PHE 0.014 0.002 PHE A 86 TYR 0.012 0.001 TYR B 27 ARG 0.007 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.421 Fit side-chains REVERT: A 128 ILE cc_start: 0.8543 (mp) cc_final: 0.8291 (mp) REVERT: A 177 MET cc_start: 0.6741 (ppp) cc_final: 0.6517 (tmm) REVERT: A 202 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8266 (mtpt) REVERT: B 34 MET cc_start: 0.8169 (tpp) cc_final: 0.7767 (mmm) REVERT: B 107 ASN cc_start: 0.8046 (p0) cc_final: 0.7709 (p0) REVERT: L 32 ASN cc_start: 0.7383 (m-40) cc_final: 0.7097 (m-40) REVERT: L 54 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7944 (tppt) outliers start: 10 outliers final: 7 residues processed: 104 average time/residue: 0.2011 time to fit residues: 24.9480 Evaluate side-chains 102 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 38 optimal weight: 0.0980 chunk 11 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3676 Z= 0.245 Angle : 0.655 7.509 4996 Z= 0.341 Chirality : 0.051 0.499 565 Planarity : 0.005 0.043 632 Dihedral : 7.225 59.577 587 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.86 % Allowed : 13.37 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.44 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.62 (0.40), residues: 162 loop : -2.10 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 104 HIS 0.003 0.001 HIS B 35 PHE 0.014 0.002 PHE A 86 TYR 0.011 0.001 TYR B 95 ARG 0.008 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.389 Fit side-chains REVERT: A 128 ILE cc_start: 0.8553 (mp) cc_final: 0.8313 (mp) REVERT: A 195 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8652 (ttpp) REVERT: A 202 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8256 (mtpt) REVERT: B 81 MET cc_start: 0.8628 (tmm) cc_final: 0.8177 (ttm) REVERT: B 107 ASN cc_start: 0.8146 (p0) cc_final: 0.7817 (p0) REVERT: L 54 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7993 (tppt) outliers start: 15 outliers final: 9 residues processed: 104 average time/residue: 0.1910 time to fit residues: 23.7080 Evaluate side-chains 102 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3676 Z= 0.388 Angle : 0.738 7.271 4996 Z= 0.388 Chirality : 0.055 0.568 565 Planarity : 0.005 0.034 632 Dihedral : 7.665 59.326 587 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 3.86 % Allowed : 16.20 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.58 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.43 (0.38), residues: 174 loop : -2.24 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 112 HIS 0.004 0.001 HIS B 35 PHE 0.022 0.002 PHE A 86 TYR 0.016 0.002 TYR B 95 ARG 0.004 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8588 (mp) cc_final: 0.8316 (mp) REVERT: A 195 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8559 (ttpp) REVERT: A 202 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8294 (mtpt) REVERT: L 88 TYR cc_start: 0.9082 (m-80) cc_final: 0.8722 (m-80) outliers start: 15 outliers final: 15 residues processed: 98 average time/residue: 0.1922 time to fit residues: 22.2622 Evaluate side-chains 107 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.0370 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.0070 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN B 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3676 Z= 0.203 Angle : 0.654 7.762 4996 Z= 0.338 Chirality : 0.050 0.465 565 Planarity : 0.004 0.032 632 Dihedral : 7.206 59.871 587 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.11 % Allowed : 17.22 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.43 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.55 (0.39), residues: 173 loop : -2.14 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.002 0.000 HIS B 35 PHE 0.011 0.001 PHE A 92 TYR 0.010 0.001 TYR A 145 ARG 0.003 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8585 (mp) cc_final: 0.8319 (mp) REVERT: A 202 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8258 (mtpt) REVERT: B 81 MET cc_start: 0.8619 (tmm) cc_final: 0.8149 (ttm) REVERT: L 88 TYR cc_start: 0.9070 (m-80) cc_final: 0.8670 (m-80) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 0.1916 time to fit residues: 22.4614 Evaluate side-chains 106 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.0170 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3676 Z= 0.261 Angle : 0.680 8.127 4996 Z= 0.351 Chirality : 0.052 0.506 565 Planarity : 0.004 0.031 632 Dihedral : 7.229 59.462 587 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.11 % Allowed : 17.48 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.45 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.56 (0.39), residues: 173 loop : -2.18 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.002 0.000 HIS B 35 PHE 0.013 0.002 PHE A 86 TYR 0.011 0.001 TYR B 95 ARG 0.004 0.001 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8580 (mp) cc_final: 0.8310 (mp) REVERT: A 177 MET cc_start: 0.6879 (ppp) cc_final: 0.6664 (tmm) REVERT: A 202 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8277 (mtpt) REVERT: B 81 MET cc_start: 0.8618 (tmm) cc_final: 0.8046 (ttm) REVERT: L 88 TYR cc_start: 0.9082 (m-80) cc_final: 0.8680 (m-80) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.1880 time to fit residues: 22.4897 Evaluate side-chains 108 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 0.0020 chunk 17 optimal weight: 0.2980 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3676 Z= 0.193 Angle : 0.654 8.240 4996 Z= 0.337 Chirality : 0.050 0.462 565 Planarity : 0.004 0.032 632 Dihedral : 7.041 58.785 587 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 3.60 % Allowed : 18.77 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.41 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.71 (0.40), residues: 161 loop : -2.12 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 92 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.001 PHE B 102 TYR 0.010 0.001 TYR A 145 ARG 0.004 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8581 (mp) cc_final: 0.8308 (mp) REVERT: A 202 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8257 (mtpt) REVERT: B 81 MET cc_start: 0.8601 (tmm) cc_final: 0.8015 (ttm) REVERT: L 62 ARG cc_start: 0.7161 (mmt-90) cc_final: 0.6659 (mmp80) REVERT: L 88 TYR cc_start: 0.9080 (m-80) cc_final: 0.8710 (m-80) outliers start: 14 outliers final: 14 residues processed: 99 average time/residue: 0.1910 time to fit residues: 22.5557 Evaluate side-chains 107 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.0470 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3676 Z= 0.238 Angle : 0.671 8.346 4996 Z= 0.346 Chirality : 0.051 0.489 565 Planarity : 0.004 0.032 632 Dihedral : 7.072 59.314 587 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.60 % Allowed : 19.02 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.43 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.72 (0.40), residues: 161 loop : -2.15 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 92 HIS 0.003 0.000 HIS B 35 PHE 0.012 0.002 PHE A 86 TYR 0.010 0.001 TYR B 95 ARG 0.004 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8594 (mp) cc_final: 0.8322 (mp) REVERT: A 177 MET cc_start: 0.6824 (ppp) cc_final: 0.6580 (tmm) REVERT: A 187 LYS cc_start: 0.7099 (mmmt) cc_final: 0.6863 (mmmt) REVERT: A 202 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8272 (mtpt) REVERT: B 34 MET cc_start: 0.8270 (tpp) cc_final: 0.7846 (mmm) REVERT: B 81 MET cc_start: 0.8601 (tmm) cc_final: 0.8031 (ttm) REVERT: L 62 ARG cc_start: 0.7165 (mmt-90) cc_final: 0.6650 (mmp80) REVERT: L 88 TYR cc_start: 0.9086 (m-80) cc_final: 0.8710 (m-80) outliers start: 14 outliers final: 14 residues processed: 95 average time/residue: 0.1867 time to fit residues: 21.1911 Evaluate side-chains 105 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 66.5218 > 50: distance: 11 - 15: 10.814 distance: 15 - 16: 9.730 distance: 15 - 139: 9.886 distance: 16 - 17: 30.894 distance: 16 - 19: 21.276 distance: 17 - 18: 11.687 distance: 17 - 20: 49.011 distance: 20 - 21: 23.451 distance: 21 - 22: 31.073 distance: 21 - 24: 28.256 distance: 22 - 23: 11.792 distance: 22 - 25: 15.827 distance: 25 - 26: 24.902 distance: 25 - 31: 17.673 distance: 26 - 27: 16.653 distance: 26 - 29: 6.007 distance: 27 - 32: 6.388 distance: 29 - 30: 28.006 distance: 30 - 31: 19.305 distance: 32 - 33: 6.269 distance: 33 - 34: 24.601 distance: 34 - 35: 37.247 distance: 34 - 36: 23.641 distance: 36 - 37: 4.940 distance: 37 - 38: 7.145 distance: 37 - 40: 13.300 distance: 38 - 39: 14.290 distance: 38 - 45: 12.191 distance: 40 - 41: 6.555 distance: 41 - 42: 12.019 distance: 42 - 43: 10.353 distance: 42 - 44: 6.202 distance: 45 - 46: 13.793 distance: 46 - 47: 7.085 distance: 46 - 49: 24.926 distance: 47 - 48: 25.109 distance: 47 - 54: 4.727 distance: 49 - 50: 17.149 distance: 50 - 51: 9.813 distance: 51 - 52: 17.433 distance: 52 - 53: 11.427 distance: 54 - 55: 16.461 distance: 55 - 56: 12.399 distance: 55 - 58: 12.399 distance: 56 - 57: 25.937 distance: 56 - 61: 10.647 distance: 58 - 59: 7.034 distance: 58 - 60: 28.905 distance: 61 - 62: 11.251 distance: 62 - 63: 9.079 distance: 62 - 65: 15.244 distance: 63 - 64: 13.978 distance: 63 - 68: 3.507 distance: 65 - 66: 19.894 distance: 65 - 67: 30.929 distance: 68 - 69: 11.271 distance: 68 - 104: 11.514 distance: 69 - 70: 15.128 distance: 69 - 72: 14.674 distance: 70 - 71: 15.713 distance: 70 - 76: 14.806 distance: 71 - 101: 9.433 distance: 72 - 73: 12.267 distance: 72 - 74: 16.272 distance: 73 - 75: 19.311 distance: 76 - 77: 24.684 distance: 77 - 78: 29.916 distance: 77 - 80: 32.282 distance: 78 - 79: 15.975 distance: 78 - 82: 22.885 distance: 80 - 81: 40.680