Starting phenix.real_space_refine on Thu Dec 7 19:12:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/12_2023/7yhp_33835_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/12_2023/7yhp_33835.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/12_2023/7yhp_33835_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/12_2023/7yhp_33835_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/12_2023/7yhp_33835_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/12_2023/7yhp_33835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/12_2023/7yhp_33835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/12_2023/7yhp_33835_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/12_2023/7yhp_33835_updated.pdb" } resolution = 3.1 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= 0.001 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 38 5.49 5 S 21 5.16 5 C 2310 2.51 5 N 687 2.21 5 O 755 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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3815 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3028 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 21, 'TRANS': 352} Chain breaks: 4 Chain: "B" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 434 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "C" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1829 SG CYS A1054 20.379 29.195 44.503 1.00 39.23 S ATOM 1715 SG CYS A1038 25.319 32.541 43.195 1.00 34.11 S ATOM 1767 SG CYS A1045 22.505 32.740 49.043 1.00 36.39 S ATOM 1786 SG CYS A1048 19.860 35.961 44.189 1.00 37.83 S Time building chain proxies: 2.95, per 1000 atoms: 0.77 Number of scatterers: 3815 At special positions: 0 Unit cell: (69.472, 88.176, 88.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 21 16.00 P 38 15.00 O 755 8.00 N 687 7.00 C 2310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.90 Conformation dependent library (CDL) restraints added in 620.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1401 " pdb="FE1 SF4 A1401 " - pdb=" SG CYS A1054 " pdb="FE4 SF4 A1401 " - pdb=" SG CYS A1048 " pdb="FE3 SF4 A1401 " - pdb=" SG CYS A1045 " pdb="FE2 SF4 A1401 " - pdb=" SG CYS A1038 " Number of angles added : 12 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 2 sheets defined 48.4% alpha, 4.5% beta 10 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 561 through 583 removed outlier: 3.646A pdb=" N PHE A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 611 through 624 Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 901 through 903 No H-bonds generated for 'chain 'A' and resid 901 through 903' Processing helix chain 'A' and resid 906 through 924 Processing helix chain 'A' and resid 930 through 933 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 1006 through 1015 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1020 through 1036 Processing helix chain 'A' and resid 1051 through 1053 No H-bonds generated for 'chain 'A' and resid 1051 through 1053' Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 4.662A pdb=" N GLN A1217 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1290 Processing helix chain 'A' and resid 1295 through 1298 Processing helix chain 'A' and resid 1310 through 1314 Processing helix chain 'A' and resid 1338 through 1341 No H-bonds generated for 'chain 'A' and resid 1338 through 1341' Processing helix chain 'A' and resid 1347 through 1355 Processing sheet with id= A, first strand: chain 'A' and resid 1206 through 1208 removed outlier: 4.086A pdb=" N TYR A1229 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1363 through 1365 removed outlier: 3.604A pdb=" N GLY A1370 " --> pdb=" O ASP A1365 " (cutoff:3.500A) 107 hydrogen bonds defined for protein. 306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 1741 1.42 - 1.64: 2212 1.64 - 1.85: 24 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 3989 Sorted by residual: bond pdb=" C3' 5CM C 26 " pdb=" C2' 5CM C 26 " ideal model delta sigma weight residual 1.323 1.516 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" O4' 5CM C 26 " pdb=" C1' 5CM C 26 " ideal model delta sigma weight residual 1.587 1.431 0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C4' 5CM C 26 " pdb=" O4' 5CM C 26 " ideal model delta sigma weight residual 1.279 1.432 -0.153 2.00e-02 2.50e+03 5.82e+01 bond pdb=" C1' 5CM C 26 " pdb=" N1 5CM C 26 " ideal model delta sigma weight residual 1.321 1.466 -0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" C2 5CM C 26 " pdb=" N3 5CM C 26 " ideal model delta sigma weight residual 1.494 1.349 0.145 2.00e-02 2.50e+03 5.22e+01 ... (remaining 3984 not shown) Histogram of bond angle deviations from ideal: 73.66 - 85.73: 12 85.73 - 97.80: 0 97.80 - 109.86: 884 109.86 - 121.93: 3858 121.93 - 133.99: 812 Bond angle restraints: 5566 Sorted by residual: angle pdb=" N THR A1299 " pdb=" CA THR A1299 " pdb=" C THR A1299 " ideal model delta sigma weight residual 113.16 107.09 6.07 1.24e+00 6.50e-01 2.40e+01 angle pdb=" N LEU A 952 " pdb=" CA LEU A 952 " pdb=" C LEU A 952 " ideal model delta sigma weight residual 111.28 116.56 -5.28 1.09e+00 8.42e-01 2.35e+01 angle pdb=" CA TYR A1300 " pdb=" CB TYR A1300 " pdb=" CG TYR A1300 " ideal model delta sigma weight residual 113.90 120.76 -6.86 1.80e+00 3.09e-01 1.45e+01 angle pdb=" OP1 5CM C 26 " pdb=" P 5CM C 26 " pdb=" OP2 5CM C 26 " ideal model delta sigma weight residual 109.44 118.72 -9.28 3.00e+00 1.11e-01 9.58e+00 angle pdb=" C TYR A1300 " pdb=" CA TYR A1300 " pdb=" CB TYR A1300 " ideal model delta sigma weight residual 110.38 105.52 4.86 2.04e+00 2.40e-01 5.67e+00 ... (remaining 5561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.68: 2057 28.68 - 57.36: 197 57.36 - 86.04: 16 86.04 - 114.72: 0 114.72 - 143.41: 1 Dihedral angle restraints: 2271 sinusoidal: 1187 harmonic: 1084 Sorted by residual: dihedral pdb=" C4' DT C 17 " pdb=" C3' DT C 17 " pdb=" O3' DT C 17 " pdb=" P DT C 18 " ideal model delta sinusoidal sigma weight residual 220.00 76.59 143.41 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" CA ARG A 903 " pdb=" CB ARG A 903 " pdb=" CG ARG A 903 " pdb=" CD ARG A 903 " ideal model delta sinusoidal sigma weight residual -60.00 -114.87 54.87 3 1.50e+01 4.44e-03 9.31e+00 dihedral pdb=" CA LEU A 952 " pdb=" CB LEU A 952 " pdb=" CG LEU A 952 " pdb=" CD1 LEU A 952 " ideal model delta sinusoidal sigma weight residual 180.00 133.27 46.73 3 1.50e+01 4.44e-03 8.38e+00 ... (remaining 2268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 530 0.049 - 0.098: 66 0.098 - 0.148: 12 0.148 - 0.197: 2 0.197 - 0.246: 1 Chirality restraints: 611 Sorted by residual: chirality pdb=" CA LEU A 952 " pdb=" N LEU A 952 " pdb=" C LEU A 952 " pdb=" CB LEU A 952 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ASN A1297 " pdb=" N ASN A1297 " pdb=" C ASN A1297 " pdb=" CB ASN A1297 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" C3' 5CM C 26 " pdb=" C4' 5CM C 26 " pdb=" O3' 5CM C 26 " pdb=" C2' 5CM C 26 " both_signs ideal model delta sigma weight residual False -2.49 -2.65 0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 608 not shown) Planarity restraints: 572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1300 " 0.028 2.00e-02 2.50e+03 1.62e-02 5.24e+00 pdb=" CG TYR A1300 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A1300 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A1300 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A1300 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A1300 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A1300 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A1300 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 950 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C LEU A 950 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 950 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY A 951 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1296 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C LEU A1296 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU A1296 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A1297 " 0.008 2.00e-02 2.50e+03 ... (remaining 569 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1160 2.84 - 3.35: 3393 3.35 - 3.87: 6556 3.87 - 4.38: 7916 4.38 - 4.90: 12404 Nonbonded interactions: 31429 Sorted by model distance: nonbonded pdb=" NE2 HIS A 581 " pdb=" OD1 ASP A 586 " model vdw 2.320 2.520 nonbonded pdb=" OE1 GLN A 624 " pdb=" OG1 THR A 899 " model vdw 2.325 2.440 nonbonded pdb=" O LEU A 582 " pdb=" NE1 TRP A1355 " model vdw 2.335 2.520 nonbonded pdb=" N2 DG B 22 " pdb=" O2 DC C 19 " model vdw 2.338 2.520 nonbonded pdb=" OG SER A 926 " pdb=" OD1 ASP A 928 " model vdw 2.355 2.440 ... (remaining 31424 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 12.530 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.630 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 0.193 3989 Z= 0.411 Angle : 0.546 9.284 5566 Z= 0.307 Chirality : 0.037 0.246 611 Planarity : 0.004 0.029 572 Dihedral : 19.251 143.405 1565 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.81 % Allowed : 4.53 % Favored : 93.66 % 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: 0.44 (0.45), residues: 364 helix: 1.66 (0.41), residues: 172 sheet: -1.60 (1.15), residues: 20 loop : -0.90 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.013 0.001 PHE A1033 TYR 0.035 0.002 TYR A1300 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.394 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.2708 time to fit residues: 17.8985 Evaluate side-chains 41 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0395 time to fit residues: 0.8934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 971 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3989 Z= 0.170 Angle : 0.499 5.152 5566 Z= 0.279 Chirality : 0.035 0.126 611 Planarity : 0.004 0.036 572 Dihedral : 23.289 144.977 822 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.51 % Allowed : 9.06 % Favored : 89.43 % 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: 0.67 (0.45), residues: 364 helix: 1.94 (0.40), residues: 172 sheet: -0.86 (1.10), residues: 23 loop : -0.97 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 561 HIS 0.003 0.001 HIS A 612 PHE 0.012 0.001 PHE A1033 TYR 0.015 0.001 TYR A1300 ARG 0.006 0.000 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.343 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 40 average time/residue: 0.2523 time to fit residues: 11.9612 Evaluate side-chains 36 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0368 time to fit residues: 0.6387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3989 Z= 0.239 Angle : 0.543 5.358 5566 Z= 0.303 Chirality : 0.038 0.137 611 Planarity : 0.004 0.032 572 Dihedral : 23.696 143.736 822 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.51 % Allowed : 10.27 % Favored : 88.22 % 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: 0.35 (0.44), residues: 364 helix: 1.68 (0.40), residues: 171 sheet: -0.86 (1.10), residues: 23 loop : -1.16 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.017 0.002 PHE A1033 TYR 0.019 0.002 TYR A1300 ARG 0.009 0.001 ARG A1362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.413 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.2145 time to fit residues: 9.6931 Evaluate side-chains 34 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0383 time to fit residues: 0.7213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3989 Z= 0.215 Angle : 0.520 5.354 5566 Z= 0.290 Chirality : 0.036 0.127 611 Planarity : 0.004 0.039 572 Dihedral : 23.739 142.906 822 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.30 % Allowed : 12.39 % Favored : 87.31 % 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: 0.26 (0.44), residues: 364 helix: 1.57 (0.40), residues: 171 sheet: -0.82 (1.13), residues: 23 loop : -1.18 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.014 0.002 PHE A1033 TYR 0.018 0.002 TYR A1300 ARG 0.005 0.001 ARG A1362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.428 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.2769 time to fit residues: 11.5720 Evaluate side-chains 34 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0689 time to fit residues: 0.6193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3989 Z= 0.207 Angle : 0.514 5.279 5566 Z= 0.288 Chirality : 0.036 0.127 611 Planarity : 0.004 0.039 572 Dihedral : 23.792 142.512 822 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.60 % Allowed : 13.60 % Favored : 85.80 % 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: 0.21 (0.44), residues: 364 helix: 1.53 (0.40), residues: 171 sheet: -0.75 (1.14), residues: 23 loop : -1.21 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 983 HIS 0.004 0.001 HIS A 612 PHE 0.014 0.002 PHE A1033 TYR 0.018 0.002 TYR A1300 ARG 0.005 0.000 ARG A1362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.369 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 0.2133 time to fit residues: 8.8617 Evaluate side-chains 33 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 51.6251 > 50: distance: 80 - 104: 6.021 distance: 84 - 114: 7.869 distance: 92 - 126: 9.452 distance: 99 - 135: 9.222 distance: 104 - 105: 3.902 distance: 105 - 106: 3.359 distance: 106 - 107: 5.625 distance: 107 - 143: 15.310 distance: 108 - 109: 5.751 distance: 109 - 110: 5.128 distance: 109 - 111: 8.526 distance: 110 - 112: 10.138 distance: 111 - 113: 7.278 distance: 112 - 113: 4.948 distance: 115 - 116: 9.453 distance: 115 - 118: 13.301 distance: 116 - 117: 3.341 distance: 116 - 126: 7.654 distance: 117 - 151: 7.217 distance: 118 - 119: 10.119 distance: 119 - 121: 4.138 distance: 120 - 122: 5.247 distance: 121 - 123: 8.241 distance: 122 - 124: 4.636 distance: 124 - 125: 3.793 distance: 126 - 127: 5.463 distance: 127 - 128: 4.276 distance: 127 - 130: 3.937 distance: 128 - 129: 14.311 distance: 128 - 135: 5.232 distance: 129 - 158: 22.993 distance: 130 - 131: 5.569 distance: 131 - 132: 6.317 distance: 135 - 136: 4.021 distance: 136 - 137: 3.514 distance: 136 - 139: 6.999 distance: 137 - 138: 12.000 distance: 138 - 169: 19.266 distance: 139 - 140: 4.038 distance: 140 - 141: 14.649 distance: 141 - 142: 20.114 distance: 143 - 144: 5.388 distance: 144 - 145: 4.387 distance: 144 - 147: 4.248 distance: 145 - 146: 3.706 distance: 145 - 151: 6.461 distance: 146 - 173: 23.766 distance: 147 - 148: 5.813 distance: 147 - 149: 9.416 distance: 148 - 150: 18.382 distance: 151 - 152: 16.116 distance: 152 - 153: 11.040 distance: 152 - 155: 16.659 distance: 153 - 154: 10.522 distance: 153 - 158: 19.320 distance: 154 - 182: 29.470 distance: 155 - 157: 22.048 distance: 158 - 159: 13.097 distance: 159 - 160: 23.414 distance: 159 - 162: 25.643 distance: 160 - 161: 32.331 distance: 160 - 169: 17.683 distance: 162 - 163: 4.927 distance: 163 - 164: 19.316 distance: 163 - 165: 7.515 distance: 164 - 166: 5.762 distance: 165 - 167: 8.498 distance: 166 - 168: 16.436 distance: 167 - 168: 7.279 distance: 169 - 170: 51.625 distance: 170 - 171: 6.824 distance: 171 - 172: 12.484 distance: 171 - 173: 26.170 distance: 173 - 174: 9.410 distance: 174 - 175: 8.334 distance: 174 - 177: 5.375 distance: 175 - 176: 9.676 distance: 175 - 182: 3.117 distance: 177 - 178: 33.833 distance: 178 - 179: 27.901 distance: 179 - 180: 38.904 distance: 180 - 181: 47.704 distance: 182 - 183: 16.642 distance: 183 - 184: 4.137 distance: 183 - 186: 4.552 distance: 184 - 185: 17.806 distance: 184 - 189: 5.968 distance: 186 - 187: 17.454 distance: 186 - 188: 8.104