Starting phenix.real_space_refine on Mon Jan 13 17:23:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9k_34570/01_2025/8h9k_34570.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9k_34570/01_2025/8h9k_34570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9k_34570/01_2025/8h9k_34570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9k_34570/01_2025/8h9k_34570.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9k_34570/01_2025/8h9k_34570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9k_34570/01_2025/8h9k_34570.cif" } resolution = 3.51 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 2176 2.51 5 N 560 2.21 5 O 634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 3 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 3.69, per 1000 atoms: 1.09 Number of scatterers: 3381 At special positions: 0 Unit cell: (56.21, 102.93, 206.59, 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 11 16.00 O 634 8.00 N 560 7.00 C 2176 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 - 3.00 Amino acid : True - 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: 0.78 Conformation dependent library (CDL) restraints added in 495.0 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 1 sheets defined 71.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 120 removed outlier: 3.836A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'K' and resid 122 through 182 Processing helix chain 'K' and resid 194 through 206 Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.884A pdb=" N ARG L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU L 49 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.146A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.706A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 44 removed outlier: 3.800A pdb=" N LEU M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.786A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 235 hydrogen bonds defined for protein. 699 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: 0.84 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1090 1.34 - 1.46: 550 1.46 - 1.57: 1795 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" N GLU K 178 " pdb=" CA GLU K 178 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.20e-02 6.94e+03 6.84e+00 bond pdb=" C PHE M 139 " pdb=" N PRO M 140 " ideal model delta sigma weight residual 1.336 1.310 0.026 1.08e-02 8.57e+03 5.77e+00 bond pdb=" N LEU K 16 " pdb=" CA LEU K 16 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.27e-02 6.20e+03 4.84e+00 bond pdb=" CB PRO M 153 " pdb=" CG PRO M 153 " ideal model delta sigma weight residual 1.506 1.451 0.055 3.90e-02 6.57e+02 2.02e+00 bond pdb=" CB GLN M 155 " pdb=" CG GLN M 155 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.50e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 4044 1.20 - 2.40: 487 2.40 - 3.60: 107 3.60 - 4.80: 27 4.80 - 6.00: 9 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N ALA L 85 " pdb=" CA ALA L 85 " pdb=" C ALA L 85 " ideal model delta sigma weight residual 108.45 113.46 -5.01 1.26e+00 6.30e-01 1.58e+01 angle pdb=" C PHE M 127 " pdb=" N ASP M 128 " pdb=" CA ASP M 128 " ideal model delta sigma weight residual 122.38 116.38 6.00 1.81e+00 3.05e-01 1.10e+01 angle pdb=" N SER L 65 " pdb=" CA SER L 65 " pdb=" C SER L 65 " ideal model delta sigma weight residual 113.38 109.56 3.82 1.17e+00 7.31e-01 1.07e+01 angle pdb=" N GLU K 178 " pdb=" CA GLU K 178 " pdb=" C GLU K 178 " ideal model delta sigma weight residual 111.14 107.77 3.37 1.08e+00 8.57e-01 9.76e+00 angle pdb=" N ASP M 11 " pdb=" CA ASP M 11 " pdb=" C ASP M 11 " ideal model delta sigma weight residual 110.48 106.10 4.38 1.48e+00 4.57e-01 8.75e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 1861 16.81 - 33.61: 194 33.61 - 50.42: 41 50.42 - 67.23: 11 67.23 - 84.03: 6 Dihedral angle restraints: 2113 sinusoidal: 862 harmonic: 1251 Sorted by residual: dihedral pdb=" CA PHE L 100 " pdb=" C PHE L 100 " pdb=" N GLU L 101 " pdb=" CA GLU L 101 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ARG K 121 " pdb=" C ARG K 121 " pdb=" N HIS K 122 " pdb=" CA HIS K 122 " ideal model delta harmonic sigma weight residual -180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE M 10 " pdb=" C ILE M 10 " pdb=" N ASP M 11 " pdb=" CA ASP M 11 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 318 0.043 - 0.086: 144 0.086 - 0.128: 39 0.128 - 0.171: 4 0.171 - 0.214: 3 Chirality restraints: 508 Sorted by residual: chirality pdb=" CB VAL L 61 " pdb=" CA VAL L 61 " pdb=" CG1 VAL L 61 " pdb=" CG2 VAL L 61 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL K 177 " pdb=" CA VAL K 177 " pdb=" CG1 VAL K 177 " pdb=" CG2 VAL K 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA ASP K 156 " pdb=" N ASP K 156 " pdb=" C ASP K 156 " pdb=" CB ASP K 156 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 82 " -0.009 2.00e-02 2.50e+03 1.30e-02 2.98e+00 pdb=" CG PHE L 82 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE L 82 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE L 82 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE L 82 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE L 82 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU M 44 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO M 45 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO M 45 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 45 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 159 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C ILE K 159 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE K 159 " 0.010 2.00e-02 2.50e+03 pdb=" N SER K 160 " 0.009 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 232 2.72 - 3.26: 3567 3.26 - 3.81: 5391 3.81 - 4.35: 6115 4.35 - 4.90: 10122 Nonbonded interactions: 25427 Sorted by model distance: nonbonded pdb=" NH1 ARG K 154 " pdb=" O THR L 89 " model vdw 2.169 3.120 nonbonded pdb=" OG1 THR L 56 " pdb=" O GLY L 59 " model vdw 2.217 3.040 nonbonded pdb=" NE2 GLN K 162 " pdb=" O ASN M 59 " model vdw 2.217 3.120 nonbonded pdb=" NH1 ARG K 121 " pdb=" O ILE M 18 " model vdw 2.282 3.120 nonbonded pdb=" O GLU M 102 " pdb=" OG SER M 105 " model vdw 2.313 3.040 ... (remaining 25422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.610 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.400 Find NCS groups from input model: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.006 0.055 3456 Z= 0.379 Angle : 0.906 5.996 4674 Z= 0.564 Chirality : 0.051 0.214 508 Planarity : 0.005 0.041 603 Dihedral : 15.467 84.035 1299 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.35), residues: 413 helix: -1.04 (0.25), residues: 286 sheet: None (None), residues: 0 loop : -2.52 (0.52), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 53 HIS 0.005 0.001 HIS K 172 PHE 0.030 0.003 PHE L 82 TYR 0.016 0.002 TYR K 145 ARG 0.004 0.001 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7749 (tttt) REVERT: K 77 PHE cc_start: 0.8620 (t80) cc_final: 0.8265 (t80) REVERT: K 118 VAL cc_start: 0.8101 (p) cc_final: 0.7842 (p) REVERT: K 143 ARG cc_start: 0.7379 (mtt180) cc_final: 0.6898 (mtm-85) REVERT: K 146 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7505 (ttt180) REVERT: K 169 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7861 (tt0) REVERT: L 50 TYR cc_start: 0.3521 (t80) cc_final: 0.3049 (t80) REVERT: M 111 ILE cc_start: 0.8375 (mt) cc_final: 0.8143 (mt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2260 time to fit residues: 31.4598 Evaluate side-chains 78 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 98 GLN K 103 HIS K 115 GLN L 68 GLN M 136 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.131666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.112712 restraints weight = 8906.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.112905 restraints weight = 4411.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114676 restraints weight = 2527.474| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3456 Z= 0.199 Angle : 0.614 5.201 4674 Z= 0.337 Chirality : 0.043 0.177 508 Planarity : 0.005 0.042 603 Dihedral : 5.303 55.833 452 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.94 % Allowed : 13.52 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.48 (0.41), residues: 413 helix: 1.29 (0.29), residues: 291 sheet: None (None), residues: 0 loop : -2.12 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 53 HIS 0.004 0.001 HIS K 103 PHE 0.012 0.001 PHE L 93 TYR 0.016 0.001 TYR K 148 ARG 0.003 0.001 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7556 (tptt) REVERT: K 118 VAL cc_start: 0.8316 (p) cc_final: 0.8037 (p) REVERT: K 143 ARG cc_start: 0.7175 (mtt180) cc_final: 0.6884 (mtm-85) REVERT: K 145 TYR cc_start: 0.7321 (t80) cc_final: 0.7025 (t80) REVERT: K 146 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7432 (ttt180) REVERT: K 163 ASN cc_start: 0.8495 (t0) cc_final: 0.7911 (m-40) REVERT: K 169 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7754 (tt0) REVERT: L 68 GLN cc_start: 0.7607 (tp-100) cc_final: 0.7282 (tp-100) REVERT: L 87 MET cc_start: 0.7883 (mpp) cc_final: 0.7352 (mpp) REVERT: M 118 MET cc_start: 0.7841 (tmm) cc_final: 0.7607 (tpp) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.2086 time to fit residues: 23.7204 Evaluate side-chains 86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 82 PHE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN M 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.131165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.111773 restraints weight = 8837.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.113026 restraints weight = 4611.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.114101 restraints weight = 2533.623| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3456 Z= 0.179 Angle : 0.557 4.887 4674 Z= 0.304 Chirality : 0.042 0.159 508 Planarity : 0.004 0.043 603 Dihedral : 5.015 53.668 452 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.23 % Allowed : 15.21 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.48 (0.42), residues: 413 helix: 2.02 (0.30), residues: 291 sheet: None (None), residues: 0 loop : -1.69 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 53 HIS 0.007 0.001 HIS K 180 PHE 0.008 0.001 PHE L 100 TYR 0.013 0.001 TYR M 85 ARG 0.001 0.000 ARG M 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7800 (mmmt) cc_final: 0.7545 (tptm) REVERT: K 114 GLN cc_start: 0.8104 (mm110) cc_final: 0.7886 (mm-40) REVERT: K 118 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8012 (p) REVERT: K 145 TYR cc_start: 0.7481 (t80) cc_final: 0.7163 (t80) REVERT: K 146 ARG cc_start: 0.7909 (ttm170) cc_final: 0.7530 (ttt180) REVERT: K 150 GLU cc_start: 0.8258 (tt0) cc_final: 0.8022 (tt0) REVERT: K 156 ASP cc_start: 0.8380 (p0) cc_final: 0.7521 (p0) REVERT: K 163 ASN cc_start: 0.8492 (t0) cc_final: 0.7954 (m-40) REVERT: K 164 MET cc_start: 0.7339 (ttm) cc_final: 0.7065 (ttm) REVERT: L 77 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8569 (mttt) REVERT: L 87 MET cc_start: 0.7946 (mpp) cc_final: 0.7548 (mmm) REVERT: M 118 MET cc_start: 0.7870 (tmm) cc_final: 0.7612 (tpp) outliers start: 15 outliers final: 12 residues processed: 97 average time/residue: 0.2070 time to fit residues: 23.4209 Evaluate side-chains 87 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 128 GLN M 21 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.129182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107696 restraints weight = 9036.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109639 restraints weight = 4345.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110837 restraints weight = 2543.696| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3456 Z= 0.255 Angle : 0.622 9.456 4674 Z= 0.334 Chirality : 0.044 0.165 508 Planarity : 0.005 0.046 603 Dihedral : 5.195 59.794 452 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.07 % Allowed : 16.34 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.70 (0.41), residues: 413 helix: 2.13 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -1.36 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 53 HIS 0.004 0.001 HIS K 172 PHE 0.010 0.002 PHE L 82 TYR 0.008 0.001 TYR L 50 ARG 0.002 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 48 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7609 (tptm) REVERT: K 85 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8076 (tt) REVERT: K 114 GLN cc_start: 0.8088 (mm110) cc_final: 0.7839 (mm-40) REVERT: K 118 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7790 (p) REVERT: K 145 TYR cc_start: 0.7592 (t80) cc_final: 0.7278 (t80) REVERT: K 146 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7525 (ttt180) REVERT: K 150 GLU cc_start: 0.8356 (tt0) cc_final: 0.8064 (tt0) REVERT: K 156 ASP cc_start: 0.8403 (p0) cc_final: 0.7909 (p0) REVERT: L 77 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8575 (mttt) REVERT: L 87 MET cc_start: 0.7990 (mpp) cc_final: 0.7650 (mmm) REVERT: M 19 ILE cc_start: 0.8968 (mm) cc_final: 0.8616 (tp) REVERT: M 118 MET cc_start: 0.7992 (tmm) cc_final: 0.7665 (tpp) outliers start: 18 outliers final: 12 residues processed: 92 average time/residue: 0.2053 time to fit residues: 22.0341 Evaluate side-chains 86 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 21 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0064 > 50: distance: 24 - 33: 3.059 distance: 52 - 58: 5.841 distance: 58 - 59: 7.466 distance: 59 - 60: 4.545 distance: 59 - 62: 14.249 distance: 60 - 65: 6.224 distance: 62 - 63: 14.732 distance: 62 - 64: 12.290 distance: 66 - 67: 6.511 distance: 66 - 69: 3.163 distance: 67 - 68: 6.975 distance: 67 - 76: 7.791 distance: 69 - 70: 5.875 distance: 70 - 72: 3.398 distance: 71 - 73: 5.581 distance: 72 - 74: 5.888 distance: 73 - 75: 6.098 distance: 74 - 75: 4.071 distance: 76 - 77: 5.011 distance: 76 - 82: 13.714 distance: 77 - 78: 7.293 distance: 78 - 79: 11.869 distance: 78 - 83: 6.543 distance: 80 - 81: 17.786 distance: 81 - 82: 4.289 distance: 83 - 84: 7.699 distance: 84 - 85: 5.423 distance: 84 - 87: 9.587 distance: 85 - 86: 26.690 distance: 85 - 90: 21.856 distance: 87 - 88: 13.606 distance: 87 - 89: 40.003 distance: 90 - 91: 28.223 distance: 91 - 92: 10.895 distance: 91 - 94: 18.503 distance: 92 - 93: 15.757 distance: 92 - 101: 7.484 distance: 94 - 95: 13.651 distance: 95 - 96: 26.006 distance: 95 - 97: 26.316 distance: 96 - 98: 9.222 distance: 97 - 99: 8.414 distance: 98 - 100: 29.940 distance: 99 - 100: 30.106 distance: 101 - 102: 9.014 distance: 102 - 103: 14.315 distance: 102 - 105: 9.291 distance: 103 - 104: 8.968 distance: 103 - 110: 8.978 distance: 105 - 106: 9.788 distance: 106 - 107: 9.657 distance: 107 - 108: 27.803 distance: 108 - 109: 9.213 distance: 110 - 111: 3.892 distance: 111 - 112: 11.265 distance: 111 - 114: 5.012 distance: 112 - 113: 9.481 distance: 112 - 121: 8.024 distance: 114 - 115: 8.920 distance: 115 - 116: 3.822 distance: 115 - 117: 16.896 distance: 116 - 118: 8.475 distance: 117 - 119: 7.741 distance: 118 - 120: 12.277 distance: 119 - 120: 6.168 distance: 121 - 122: 6.820 distance: 122 - 123: 6.838 distance: 122 - 125: 12.569 distance: 123 - 124: 12.065 distance: 123 - 130: 22.895 distance: 125 - 126: 16.915 distance: 126 - 127: 5.323 distance: 127 - 128: 12.239 distance: 127 - 129: 3.412 distance: 130 - 131: 9.867 distance: 131 - 132: 11.505 distance: 131 - 134: 15.424 distance: 132 - 133: 4.978 distance: 132 - 138: 11.720 distance: 134 - 135: 21.409 distance: 135 - 136: 22.644 distance: 135 - 137: 19.419 distance: 138 - 139: 9.534 distance: 138 - 144: 8.363 distance: 139 - 140: 15.396 distance: 139 - 142: 18.360 distance: 140 - 141: 26.212 distance: 140 - 145: 8.559 distance: 142 - 143: 10.673 distance: 143 - 144: 18.270