Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hoe-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-3.8-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-3.8-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-3.8-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 236 and 0 Target number of residues in the AU: 236 Target solvent content: 0.6755 Checking the provided sequence file Detected sequence length: 380 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 380 Adjusted target solvent content: 0.48 Input MTZ file: 2hoe-3.8-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 151 Cell parameters: 62.599 62.599 173.950 90.000 90.000 120.000 Input sequence file: 2hoe-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3040 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 57.983 3.801 Wilson plot Bfac: 96.08 4042 reflections ( 99.75 % complete ) and 0 restraints for refining 3379 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3341 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3104 (Rfree = 0.000) for 3379 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 3426 seeds are put forward Round 1: 127 peptides, 22 chains. Longest chain 13 peptides. Score 0.358 Round 2: 167 peptides, 27 chains. Longest chain 14 peptides. Score 0.433 Round 3: 164 peptides, 25 chains. Longest chain 21 peptides. Score 0.456 Round 4: 183 peptides, 25 chains. Longest chain 20 peptides. Score 0.525 Round 5: 187 peptides, 23 chains. Longest chain 25 peptides. Score 0.569 Taking the results from Round 5 Chains 23, Residues 164, Estimated correctness of the model 0.0 % 4 chains (46 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4042 reflections ( 99.75 % complete ) and 6143 restraints for refining 2750 atoms. 5362 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2440 (Rfree = 0.000) for 2750 atoms. Found 14 (15 requested) and removed 29 (7 requested) atoms. Cycle 2: After refmac, R = 0.2250 (Rfree = 0.000) for 2685 atoms. Found 10 (15 requested) and removed 55 (7 requested) atoms. Cycle 3: After refmac, R = 0.2315 (Rfree = 0.000) for 2614 atoms. Found 9 (14 requested) and removed 30 (7 requested) atoms. Cycle 4: After refmac, R = 0.2140 (Rfree = 0.000) for 2579 atoms. Found 3 (14 requested) and removed 25 (7 requested) atoms. Cycle 5: After refmac, R = 0.2126 (Rfree = 0.000) for 2532 atoms. Found 5 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 2598 seeds are put forward Round 1: 147 peptides, 26 chains. Longest chain 13 peptides. Score 0.369 Round 2: 175 peptides, 28 chains. Longest chain 16 peptides. Score 0.448 Round 3: 187 peptides, 28 chains. Longest chain 18 peptides. Score 0.492 Round 4: 185 peptides, 25 chains. Longest chain 17 peptides. Score 0.532 Round 5: 210 peptides, 26 chains. Longest chain 15 peptides. Score 0.599 Taking the results from Round 5 Chains 30, Residues 184, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 4042 reflections ( 99.75 % complete ) and 5695 restraints for refining 2633 atoms. 4880 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2330 (Rfree = 0.000) for 2633 atoms. Found 10 (14 requested) and removed 40 (7 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1996 (Rfree = 0.000) for 2581 atoms. Found 5 (14 requested) and removed 22 (7 requested) atoms. Cycle 8: After refmac, R = 0.1933 (Rfree = 0.000) for 2549 atoms. Found 2 (14 requested) and removed 17 (7 requested) atoms. Cycle 9: After refmac, R = 0.1791 (Rfree = 0.000) for 2527 atoms. Found 9 (13 requested) and removed 12 (6 requested) atoms. Cycle 10: After refmac, R = 0.1870 (Rfree = 0.000) for 2521 atoms. Found 7 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 3.82 Search for helices and strands: 0 residues in 0 chains, 2627 seeds are put forward Round 1: 156 peptides, 29 chains. Longest chain 12 peptides. Score 0.353 Round 2: 181 peptides, 31 chains. Longest chain 15 peptides. Score 0.420 Round 3: 191 peptides, 29 chains. Longest chain 14 peptides. Score 0.491 Round 4: 189 peptides, 26 chains. Longest chain 19 peptides. Score 0.531 Round 5: 193 peptides, 29 chains. Longest chain 25 peptides. Score 0.498 Taking the results from Round 4 Chains 29, Residues 163, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 4042 reflections ( 99.75 % complete ) and 5713 restraints for refining 2657 atoms. 4998 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2475 (Rfree = 0.000) for 2657 atoms. Found 14 (14 requested) and removed 78 (7 requested) atoms. Cycle 12: After refmac, R = 0.2384 (Rfree = 0.000) for 2573 atoms. Found 14 (14 requested) and removed 32 (7 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1913 (Rfree = 0.000) for 2544 atoms. Found 6 (14 requested) and removed 17 (7 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1785 (Rfree = 0.000) for 2522 atoms. Found 4 (13 requested) and removed 16 (6 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1773 (Rfree = 0.000) for 2507 atoms. Found 1 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 2580 seeds are put forward Round 1: 150 peptides, 29 chains. Longest chain 11 peptides. Score 0.327 Round 2: 168 peptides, 27 chains. Longest chain 13 peptides. Score 0.437 Round 3: 167 peptides, 26 chains. Longest chain 14 peptides. Score 0.450 Round 4: 162 peptides, 24 chains. Longest chain 15 peptides. Score 0.465 Round 5: 161 peptides, 27 chains. Longest chain 10 peptides. Score 0.409 Taking the results from Round 4 Chains 24, Residues 138, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4042 reflections ( 99.75 % complete ) and 5875 restraints for refining 2594 atoms. 5335 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2437 (Rfree = 0.000) for 2594 atoms. Found 10 (14 requested) and removed 17 (7 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2186 (Rfree = 0.000) for 2575 atoms. Found 7 (14 requested) and removed 21 (7 requested) atoms. Cycle 18: After refmac, R = 0.2040 (Rfree = 0.000) for 2554 atoms. Found 7 (14 requested) and removed 12 (7 requested) atoms. Cycle 19: After refmac, R = 0.1679 (Rfree = 0.000) for 2545 atoms. Found 1 (14 requested) and removed 10 (7 requested) atoms. Cycle 20: After refmac, R = 0.1585 (Rfree = 0.000) for 2536 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 2626 seeds are put forward Round 1: 148 peptides, 31 chains. Longest chain 8 peptides. Score 0.281 Round 2: 160 peptides, 27 chains. Longest chain 13 peptides. Score 0.405 Round 3: 162 peptides, 24 chains. Longest chain 19 peptides. Score 0.465 Round 4: 172 peptides, 28 chains. Longest chain 18 peptides. Score 0.436 Round 5: 166 peptides, 27 chains. Longest chain 16 peptides. Score 0.429 Taking the results from Round 3 Chains 24, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4042 reflections ( 99.75 % complete ) and 5975 restraints for refining 2598 atoms. 5447 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2232 (Rfree = 0.000) for 2598 atoms. Found 6 (14 requested) and removed 25 (7 requested) atoms. Cycle 22: After refmac, R = 0.2160 (Rfree = 0.000) for 2572 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 23: After refmac, R = 0.1996 (Rfree = 0.000) for 2562 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1877 (Rfree = 0.000) for 2557 atoms. Found 12 (14 requested) and removed 14 (7 requested) atoms. Cycle 25: After refmac, R = 0.1497 (Rfree = 0.000) for 2551 atoms. Found 4 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 2641 seeds are put forward Round 1: 140 peptides, 27 chains. Longest chain 15 peptides. Score 0.320 Round 2: 163 peptides, 29 chains. Longest chain 15 peptides. Score 0.382 Round 3: 171 peptides, 28 chains. Longest chain 15 peptides. Score 0.432 Round 4: 173 peptides, 26 chains. Longest chain 16 peptides. Score 0.473 Round 5: 186 peptides, 29 chains. Longest chain 15 peptides. Score 0.473 Taking the results from Round 5 Chains 29, Residues 157, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4042 reflections ( 99.75 % complete ) and 6136 restraints for refining 2746 atoms. 5523 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1941 (Rfree = 0.000) for 2746 atoms. Found 8 (15 requested) and removed 14 (7 requested) atoms. Cycle 27: After refmac, R = 0.1949 (Rfree = 0.000) for 2722 atoms. Found 6 (15 requested) and removed 12 (7 requested) atoms. Cycle 28: After refmac, R = 0.1514 (Rfree = 0.000) for 2702 atoms. Found 2 (14 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1668 (Rfree = 0.000) for 2693 atoms. Found 3 (14 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.1707 (Rfree = 0.000) for 2682 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 2779 seeds are put forward Round 1: 123 peptides, 26 chains. Longest chain 8 peptides. Score 0.261 Round 2: 148 peptides, 27 chains. Longest chain 9 peptides. Score 0.355 Round 3: 157 peptides, 26 chains. Longest chain 12 peptides. Score 0.411 Round 4: 145 peptides, 26 chains. Longest chain 10 peptides. Score 0.361 Round 5: 148 peptides, 25 chains. Longest chain 11 peptides. Score 0.392 Taking the results from Round 3 Chains 26, Residues 131, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4042 reflections ( 99.75 % complete ) and 6357 restraints for refining 2748 atoms. 5840 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2048 (Rfree = 0.000) for 2748 atoms. Found 9 (15 requested) and removed 14 (7 requested) atoms. Cycle 32: After refmac, R = 0.1986 (Rfree = 0.000) for 2719 atoms. Found 4 (15 requested) and removed 13 (7 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2085 (Rfree = 0.000) for 2704 atoms. Found 10 (14 requested) and removed 13 (7 requested) atoms. Cycle 34: After refmac, R = 0.1774 (Rfree = 0.000) for 2695 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Cycle 35: After refmac, R = 0.1806 (Rfree = 0.000) for 2682 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 2803 seeds are put forward Round 1: 127 peptides, 30 chains. Longest chain 7 peptides. Score 0.201 Round 2: 149 peptides, 27 chains. Longest chain 12 peptides. Score 0.359 Round 3: 150 peptides, 25 chains. Longest chain 14 peptides. Score 0.400 Round 4: 148 peptides, 26 chains. Longest chain 11 peptides. Score 0.373 Round 5: 153 peptides, 25 chains. Longest chain 13 peptides. Score 0.412 Taking the results from Round 5 Chains 25, Residues 128, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4042 reflections ( 99.75 % complete ) and 6407 restraints for refining 2750 atoms. 5920 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2035 (Rfree = 0.000) for 2750 atoms. Found 12 (15 requested) and removed 11 (7 requested) atoms. Cycle 37: After refmac, R = 0.2104 (Rfree = 0.000) for 2742 atoms. Found 11 (15 requested) and removed 14 (7 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1850 (Rfree = 0.000) for 2731 atoms. Found 10 (15 requested) and removed 16 (7 requested) atoms. Cycle 39: After refmac, R = 0.2120 (Rfree = 0.000) for 2718 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 40: After refmac, R = 0.1904 (Rfree = 0.000) for 2714 atoms. Found 12 (14 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 2819 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 9 peptides. Score 0.259 Round 2: 102 peptides, 19 chains. Longest chain 11 peptides. Score 0.303 Round 3: 115 peptides, 20 chains. Longest chain 9 peptides. Score 0.343 Round 4: 129 peptides, 21 chains. Longest chain 13 peptides. Score 0.386 Round 5: 125 peptides, 19 chains. Longest chain 22 peptides. Score 0.406 Taking the results from Round 5 Chains 19, Residues 106, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4042 reflections ( 99.75 % complete ) and 6477 restraints for refining 2750 atoms. 6072 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1957 (Rfree = 0.000) for 2750 atoms. Found 10 (15 requested) and removed 13 (7 requested) atoms. Cycle 42: After refmac, R = 0.1921 (Rfree = 0.000) for 2735 atoms. Found 13 (15 requested) and removed 8 (7 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1873 (Rfree = 0.000) for 2736 atoms. Found 12 (15 requested) and removed 15 (7 requested) atoms. Cycle 44: After refmac, R = 0.1720 (Rfree = 0.000) for 2722 atoms. Found 8 (15 requested) and removed 8 (7 requested) atoms. Cycle 45: After refmac, R = 0.1852 (Rfree = 0.000) for 2715 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 2805 seeds are put forward Round 1: 96 peptides, 20 chains. Longest chain 7 peptides. Score 0.253 Round 2: 122 peptides, 22 chains. Longest chain 8 peptides. Score 0.336 Round 3: 129 peptides, 22 chains. Longest chain 11 peptides. Score 0.367 Round 4: 134 peptides, 23 chains. Longest chain 10 peptides. Score 0.369 Round 5: 126 peptides, 21 chains. Longest chain 10 peptides. Score 0.373 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 105, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hoe-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4042 reflections ( 99.75 % complete ) and 6491 restraints for refining 2735 atoms. 6092 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1793 (Rfree = 0.000) for 2735 atoms. Found 0 (15 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.1866 (Rfree = 0.000) for 2717 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.1683 (Rfree = 0.000) for 2705 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.1283 (Rfree = 0.000) for 2698 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 53.29