Starting phenix.real_space_refine on Mon Mar 11 14:31:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w64_21552/03_2024/6w64_21552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w64_21552/03_2024/6w64_21552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w64_21552/03_2024/6w64_21552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w64_21552/03_2024/6w64_21552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w64_21552/03_2024/6w64_21552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w64_21552/03_2024/6w64_21552.pdb" } resolution = 3.9 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= 0.003 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: 5 Type Number sf(0) Gaussians P 56 5.49 5 S 34 5.16 5 C 5213 2.51 5 N 1474 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A ARG 965": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8505 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7331 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 32, 'TRANS': 895} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 805 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 13, 'rna3p_pyr': 14} Link IDs: {'rna2p': 11, 'rna3p': 26} Chain: "C" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 6.02, per 1000 atoms: 0.71 Number of scatterers: 8505 At special positions: 0 Unit cell: (85.05, 128.1, 108.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 56 15.00 O 1728 8.00 N 1474 7.00 C 5213 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: 3.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 55.7% alpha, 7.2% beta 13 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.630A pdb=" N LEU A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 297 through 332 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 371 through 393 removed outlier: 4.539A pdb=" N THR A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 422 Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 708 through 721 removed outlier: 3.804A pdb=" N LYS A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 747 removed outlier: 3.531A pdb=" N ILE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 771 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.569A pdb=" N ALA A 775 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 787 Processing helix chain 'A' and resid 800 through 822 Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 846 through 886 Processing helix chain 'A' and resid 905 through 914 removed outlier: 3.638A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 929 Processing helix chain 'A' and resid 967 through 971 Processing helix chain 'A' and resid 972 through 984 Processing helix chain 'A' and resid 990 through 1008 Processing helix chain 'A' and resid 1010 through 1015 Processing helix chain 'A' and resid 1018 through 1033 Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1085 through 1090 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 7.423A pdb=" N ASN A 477 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY A 486 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 479 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE A 488 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU A 485 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 523 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 530 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.595A pdb=" N LYS A 81 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 683 removed outlier: 6.268A pdb=" N GLU A 660 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 680 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 669 through 670 Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 689 Processing sheet with id=AA6, first strand: chain 'A' and resid 893 through 894 removed outlier: 7.012A pdb=" N GLY A 893 " --> pdb=" O VAL A 939 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1049 through 1050 406 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1268 1.28 - 1.41: 2320 1.41 - 1.54: 5026 1.54 - 1.68: 118 1.68 - 1.81: 58 Bond restraints: 8790 Sorted by residual: bond pdb=" C PHE A 80 " pdb=" O PHE A 80 " ideal model delta sigma weight residual 1.233 1.148 0.084 1.12e-02 7.97e+03 5.68e+01 bond pdb=" N ARG A 962 " pdb=" CA ARG A 962 " ideal model delta sigma weight residual 1.454 1.493 -0.038 1.17e-02 7.31e+03 1.07e+01 bond pdb=" N LYS A 81 " pdb=" CA LYS A 81 " ideal model delta sigma weight residual 1.454 1.493 -0.040 1.23e-02 6.61e+03 1.03e+01 bond pdb=" C ASN A1064 " pdb=" N GLY A1065 " ideal model delta sigma weight residual 1.331 1.376 -0.046 1.46e-02 4.69e+03 9.74e+00 bond pdb=" N GLY A 682 " pdb=" CA GLY A 682 " ideal model delta sigma weight residual 1.448 1.480 -0.031 1.00e-02 1.00e+04 9.62e+00 ... (remaining 8785 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.92: 515 106.92 - 113.68: 4917 113.68 - 120.44: 3425 120.44 - 127.20: 3072 127.20 - 133.97: 180 Bond angle restraints: 12109 Sorted by residual: angle pdb=" N PRO A 987 " pdb=" CA PRO A 987 " pdb=" CB PRO A 987 " ideal model delta sigma weight residual 103.36 110.25 -6.89 8.80e-01 1.29e+00 6.14e+01 angle pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" O PHE A 80 " ideal model delta sigma weight residual 120.89 112.15 8.74 1.27e+00 6.20e-01 4.74e+01 angle pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N LYS A 81 " ideal model delta sigma weight residual 115.75 123.12 -7.37 1.08e+00 8.57e-01 4.66e+01 angle pdb=" C ASN A1064 " pdb=" N GLY A1065 " pdb=" CA GLY A1065 " ideal model delta sigma weight residual 121.41 129.72 -8.31 1.96e+00 2.60e-01 1.80e+01 angle pdb=" O SER A 95 " pdb=" C SER A 95 " pdb=" N ASN A 96 " ideal model delta sigma weight residual 122.07 125.89 -3.82 1.03e+00 9.43e-01 1.37e+01 ... (remaining 12104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 5153 34.97 - 69.93: 195 69.93 - 104.90: 17 104.90 - 139.86: 0 139.86 - 174.83: 3 Dihedral angle restraints: 5368 sinusoidal: 2635 harmonic: 2733 Sorted by residual: dihedral pdb=" O4' U B 11 " pdb=" C1' U B 11 " pdb=" N1 U B 11 " pdb=" C2 U B 11 " ideal model delta sinusoidal sigma weight residual -160.00 -7.34 -152.66 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' U B -6 " pdb=" C1' U B -6 " pdb=" N1 U B -6 " pdb=" C2 U B -6 " ideal model delta sinusoidal sigma weight residual -128.00 46.83 -174.83 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA LYS A 487 " pdb=" C LYS A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1077 0.038 - 0.076: 212 0.076 - 0.114: 61 0.114 - 0.153: 13 0.153 - 0.191: 4 Chirality restraints: 1367 Sorted by residual: chirality pdb=" C2' A B -10 " pdb=" C3' A B -10 " pdb=" O2' A B -10 " pdb=" C1' A B -10 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA PRO A 987 " pdb=" N PRO A 987 " pdb=" C PRO A 987 " pdb=" CB PRO A 987 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" C3' C B -8 " pdb=" C4' C B -8 " pdb=" O3' C B -8 " pdb=" C2' C B -8 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 1364 not shown) Planarity restraints: 1338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 681 " -0.017 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C SER A 681 " 0.055 2.00e-02 2.50e+03 pdb=" O SER A 681 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY A 682 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 80 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C PHE A 80 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE A 80 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 81 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 96 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ASN A 96 " 0.031 2.00e-02 2.50e+03 pdb=" O ASN A 96 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 97 " -0.011 2.00e-02 2.50e+03 ... (remaining 1335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 830 2.74 - 3.28: 8889 3.28 - 3.82: 14483 3.82 - 4.36: 16738 4.36 - 4.90: 28352 Nonbonded interactions: 69292 Sorted by model distance: nonbonded pdb=" NH2 ARG A 57 " pdb=" OD1 ASP A 72 " model vdw 2.196 2.520 nonbonded pdb=" O SER A 981 " pdb=" OG SER A 984 " model vdw 2.203 2.440 nonbonded pdb=" NH1 ARG A 853 " pdb=" OE2 GLU A 857 " model vdw 2.206 2.520 nonbonded pdb=" O ASN A 96 " pdb=" ND2 ASN A 96 " model vdw 2.207 2.520 nonbonded pdb=" O TYR A 104 " pdb=" OG SER A 105 " model vdw 2.216 2.440 ... (remaining 69287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.930 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 29.610 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 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 0.084 8790 Z= 0.201 Angle : 0.577 8.742 12109 Z= 0.371 Chirality : 0.037 0.191 1367 Planarity : 0.003 0.032 1338 Dihedral : 16.240 174.826 3600 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.99 % Favored : 92.90 % Rotamer: Outliers : 1.29 % Allowed : 3.10 % Favored : 95.60 % 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: 0.30 (0.29), residues: 916 helix: 2.21 (0.24), residues: 501 sheet: -2.20 (0.54), residues: 74 loop : -2.47 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.004 0.001 HIS A 952 PHE 0.007 0.001 PHE A 911 TYR 0.024 0.001 TYR A 695 ARG 0.002 0.000 ARG A 918 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 248 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 PRO cc_start: 0.8928 (Cg_endo) cc_final: 0.8658 (Cg_exo) REVERT: A 539 GLU cc_start: 0.4956 (tp30) cc_final: 0.3804 (tp30) REVERT: A 806 MET cc_start: 0.7081 (ttp) cc_final: 0.6849 (ttp) REVERT: A 850 PHE cc_start: 0.8922 (t80) cc_final: 0.8485 (t80) REVERT: A 918 ARG cc_start: 0.6123 (mmm-85) cc_final: 0.5808 (mmm-85) REVERT: A 929 MET cc_start: 0.7473 (mtt) cc_final: 0.7213 (mtp) REVERT: A 940 ASN cc_start: 0.7558 (t0) cc_final: 0.6848 (p0) REVERT: A 1074 ASP cc_start: 0.6322 (p0) cc_final: 0.5873 (p0) outliers start: 10 outliers final: 4 residues processed: 256 average time/residue: 0.2362 time to fit residues: 79.5522 Evaluate side-chains 144 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 890 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 103 GLN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS A 471 GLN A 497 HIS A 616 ASN A 672 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8790 Z= 0.316 Angle : 0.712 13.033 12109 Z= 0.368 Chirality : 0.043 0.180 1367 Planarity : 0.004 0.029 1338 Dihedral : 19.846 177.417 1816 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.72 % Allowed : 13.07 % Favored : 84.22 % 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: -0.20 (0.29), residues: 916 helix: 1.74 (0.23), residues: 505 sheet: -2.46 (0.52), residues: 79 loop : -2.62 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 915 HIS 0.006 0.001 HIS A 384 PHE 0.022 0.002 PHE A 743 TYR 0.017 0.002 TYR A 406 ARG 0.008 0.001 ARG A 769 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6365 (tpt) cc_final: 0.5955 (tpt) REVERT: A 86 ASN cc_start: 0.8464 (p0) cc_final: 0.8232 (p0) REVERT: A 159 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6997 (tp30) REVERT: A 460 LYS cc_start: 0.8555 (tttm) cc_final: 0.8328 (ttmt) REVERT: A 918 ARG cc_start: 0.6758 (mmm-85) cc_final: 0.6397 (mmm-85) REVERT: A 940 ASN cc_start: 0.7913 (t0) cc_final: 0.7249 (p0) REVERT: A 959 PHE cc_start: 0.7689 (m-10) cc_final: 0.7477 (m-80) outliers start: 21 outliers final: 14 residues processed: 159 average time/residue: 0.2171 time to fit residues: 47.4208 Evaluate side-chains 133 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 40.0000 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 HIS ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 HIS A 895 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8790 Z= 0.369 Angle : 0.726 12.859 12109 Z= 0.379 Chirality : 0.044 0.179 1367 Planarity : 0.005 0.067 1338 Dihedral : 20.111 175.911 1811 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.88 % Allowed : 15.39 % Favored : 80.72 % 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: -0.51 (0.28), residues: 916 helix: 1.46 (0.23), residues: 505 sheet: -2.54 (0.56), residues: 74 loop : -2.74 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 915 HIS 0.005 0.002 HIS A 24 PHE 0.035 0.003 PHE A 80 TYR 0.019 0.002 TYR A 135 ARG 0.006 0.001 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6065 (tpt) cc_final: 0.5658 (tpt) REVERT: A 116 TYR cc_start: 0.8631 (t80) cc_final: 0.8212 (t80) REVERT: A 159 GLU cc_start: 0.7216 (mm-30) cc_final: 0.7008 (tp30) REVERT: A 315 MET cc_start: 0.7832 (mmt) cc_final: 0.7523 (mmt) REVERT: A 460 LYS cc_start: 0.8568 (tttm) cc_final: 0.8357 (ttmt) REVERT: A 539 GLU cc_start: 0.4755 (tp30) cc_final: 0.3414 (tp30) REVERT: A 646 TYR cc_start: 0.7682 (p90) cc_final: 0.7301 (p90) REVERT: A 806 MET cc_start: 0.7472 (ttp) cc_final: 0.7115 (ptp) REVERT: A 940 ASN cc_start: 0.8021 (t0) cc_final: 0.7465 (p0) REVERT: A 1043 ARG cc_start: 0.6097 (mpt180) cc_final: 0.4931 (tpp80) outliers start: 30 outliers final: 22 residues processed: 156 average time/residue: 0.2085 time to fit residues: 45.4045 Evaluate side-chains 137 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 TRP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 HIS ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8790 Z= 0.219 Angle : 0.629 13.295 12109 Z= 0.324 Chirality : 0.041 0.162 1367 Planarity : 0.004 0.032 1338 Dihedral : 19.993 176.010 1811 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.85 % Allowed : 16.43 % Favored : 80.72 % 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: -0.39 (0.28), residues: 916 helix: 1.63 (0.23), residues: 504 sheet: -2.47 (0.51), residues: 92 loop : -2.78 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 915 HIS 0.007 0.001 HIS A 528 PHE 0.022 0.002 PHE A 743 TYR 0.017 0.002 TYR A 542 ARG 0.004 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6069 (tpt) cc_final: 0.5674 (tpt) REVERT: A 37 LEU cc_start: 0.8286 (mt) cc_final: 0.7883 (mt) REVERT: A 116 TYR cc_start: 0.8486 (t80) cc_final: 0.8042 (t80) REVERT: A 159 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6834 (tp30) REVERT: A 315 MET cc_start: 0.7793 (mmt) cc_final: 0.7429 (mmt) REVERT: A 335 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.6436 (m-10) REVERT: A 460 LYS cc_start: 0.8535 (tttm) cc_final: 0.8332 (ttmt) REVERT: A 537 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6407 (mm) REVERT: A 539 GLU cc_start: 0.4833 (tp30) cc_final: 0.3560 (tp30) REVERT: A 646 TYR cc_start: 0.7590 (p90) cc_final: 0.7239 (p90) REVERT: A 918 ARG cc_start: 0.6762 (mmm-85) cc_final: 0.6373 (mmm-85) REVERT: A 940 ASN cc_start: 0.7988 (t0) cc_final: 0.7427 (p0) outliers start: 22 outliers final: 15 residues processed: 150 average time/residue: 0.1956 time to fit residues: 41.3477 Evaluate side-chains 138 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 0.0000 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 overall best weight: 2.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 518 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8790 Z= 0.295 Angle : 0.667 13.199 12109 Z= 0.348 Chirality : 0.043 0.183 1367 Planarity : 0.004 0.034 1338 Dihedral : 20.057 175.949 1811 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.23 % Allowed : 17.21 % Favored : 79.56 % 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: -0.57 (0.28), residues: 916 helix: 1.46 (0.23), residues: 505 sheet: -2.63 (0.48), residues: 96 loop : -2.79 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 915 HIS 0.006 0.001 HIS A 952 PHE 0.024 0.002 PHE A 743 TYR 0.015 0.002 TYR A 301 ARG 0.003 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6309 (tpt) cc_final: 0.5880 (tpt) REVERT: A 37 LEU cc_start: 0.8300 (mt) cc_final: 0.8045 (mt) REVERT: A 86 ASN cc_start: 0.8364 (p0) cc_final: 0.8013 (p0) REVERT: A 159 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6726 (tp30) REVERT: A 315 MET cc_start: 0.7797 (mmt) cc_final: 0.7548 (mmt) REVERT: A 335 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.6465 (m-10) REVERT: A 460 LYS cc_start: 0.8570 (tttm) cc_final: 0.8369 (ttmt) REVERT: A 476 PHE cc_start: 0.7451 (m-80) cc_final: 0.7208 (m-80) REVERT: A 539 GLU cc_start: 0.4629 (tp30) cc_final: 0.3224 (tp30) REVERT: A 646 TYR cc_start: 0.7681 (p90) cc_final: 0.7315 (p90) REVERT: A 780 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7279 (pt0) REVERT: A 940 ASN cc_start: 0.7975 (t0) cc_final: 0.7441 (p0) REVERT: A 1043 ARG cc_start: 0.6105 (mmt180) cc_final: 0.4990 (tpp80) outliers start: 25 outliers final: 18 residues processed: 144 average time/residue: 0.1806 time to fit residues: 37.6083 Evaluate side-chains 138 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 951 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 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 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN A 480 ASN A 616 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8790 Z= 0.177 Angle : 0.606 12.875 12109 Z= 0.310 Chirality : 0.040 0.213 1367 Planarity : 0.003 0.032 1338 Dihedral : 19.911 176.256 1811 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.36 % Allowed : 18.24 % Favored : 78.40 % 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: -0.34 (0.29), residues: 916 helix: 1.72 (0.23), residues: 505 sheet: -2.47 (0.48), residues: 98 loop : -2.84 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 915 HIS 0.001 0.000 HIS A 150 PHE 0.020 0.002 PHE A 743 TYR 0.012 0.001 TYR A 406 ARG 0.003 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 MET cc_start: 0.6137 (tpt) cc_final: 0.5709 (tpt) REVERT: A 37 LEU cc_start: 0.8261 (mt) cc_final: 0.8024 (mt) REVERT: A 159 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6761 (tp30) REVERT: A 315 MET cc_start: 0.7639 (mmt) cc_final: 0.7322 (mmt) REVERT: A 335 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.6053 (m-10) REVERT: A 460 LYS cc_start: 0.8482 (tttm) cc_final: 0.8273 (ttmt) REVERT: A 539 GLU cc_start: 0.4648 (tp30) cc_final: 0.3461 (tp30) REVERT: A 646 TYR cc_start: 0.7576 (p90) cc_final: 0.7333 (p90) REVERT: A 786 LEU cc_start: 0.7160 (mt) cc_final: 0.6774 (mt) REVERT: A 915 TRP cc_start: 0.7442 (t60) cc_final: 0.7157 (t60) REVERT: A 918 ARG cc_start: 0.6797 (mmm-85) cc_final: 0.6455 (mmm-85) REVERT: A 940 ASN cc_start: 0.7859 (t0) cc_final: 0.7377 (p0) REVERT: A 1043 ARG cc_start: 0.6185 (mmt180) cc_final: 0.5780 (tpp80) outliers start: 26 outliers final: 15 residues processed: 147 average time/residue: 0.1969 time to fit residues: 40.7462 Evaluate side-chains 133 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 873 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 55.6756 > 50: distance: 49 - 53: 32.593 distance: 53 - 54: 22.047 distance: 54 - 55: 23.566 distance: 54 - 57: 31.699 distance: 55 - 56: 21.015 distance: 55 - 62: 20.839 distance: 57 - 58: 32.819 distance: 58 - 59: 27.113 distance: 59 - 60: 15.604 distance: 60 - 61: 18.387 distance: 62 - 63: 8.568 distance: 63 - 64: 28.444 distance: 63 - 66: 20.430 distance: 64 - 65: 14.129 distance: 64 - 70: 21.996 distance: 66 - 67: 23.967 distance: 67 - 68: 14.549 distance: 67 - 69: 48.840 distance: 70 - 71: 13.477 distance: 71 - 72: 32.258 distance: 71 - 74: 13.408 distance: 72 - 73: 21.743 distance: 72 - 78: 21.405 distance: 73 - 183: 22.680 distance: 74 - 75: 30.143 distance: 75 - 76: 29.213 distance: 75 - 77: 13.707 distance: 78 - 79: 11.150 distance: 79 - 80: 22.764 distance: 80 - 81: 19.622 distance: 80 - 82: 20.681 distance: 82 - 83: 9.204 distance: 82 - 174: 14.667 distance: 83 - 84: 6.236 distance: 83 - 86: 14.983 distance: 84 - 85: 19.812 distance: 84 - 91: 35.987 distance: 85 - 171: 28.428 distance: 86 - 87: 13.451 distance: 87 - 88: 3.750 distance: 88 - 89: 26.250 distance: 89 - 90: 11.399 distance: 91 - 92: 7.165 distance: 92 - 93: 27.763 distance: 92 - 95: 35.337 distance: 93 - 94: 19.139 distance: 93 - 99: 25.770 distance: 95 - 96: 33.425 distance: 95 - 97: 13.498 distance: 96 - 98: 45.657 distance: 99 - 100: 26.118 distance: 100 - 101: 17.039 distance: 100 - 103: 18.002 distance: 101 - 102: 27.477 distance: 101 - 107: 15.494 distance: 103 - 104: 26.484 distance: 103 - 105: 18.769 distance: 104 - 106: 29.278 distance: 107 - 108: 10.972 distance: 108 - 109: 22.649 distance: 108 - 111: 14.245 distance: 109 - 110: 11.854 distance: 109 - 113: 15.339 distance: 110 - 137: 25.878 distance: 111 - 112: 11.941 distance: 113 - 114: 9.133 distance: 113 - 119: 18.526 distance: 114 - 115: 9.385 distance: 114 - 117: 19.337 distance: 115 - 116: 13.088 distance: 115 - 120: 14.092 distance: 116 - 144: 19.268 distance: 117 - 118: 13.149 distance: 118 - 119: 22.331 distance: 120 - 121: 6.594 distance: 121 - 122: 10.127 distance: 121 - 124: 8.076 distance: 122 - 123: 5.585 distance: 122 - 129: 16.171 distance: 123 - 152: 14.832 distance: 124 - 125: 20.838 distance: 125 - 126: 8.548 distance: 126 - 127: 7.884 distance: 127 - 128: 12.342