null Sun 23 Dec 22:22:42 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 1vqz-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqz-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-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/1vqz-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-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 ============================================================ Sun 23 Dec 22:22:51 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/1vqz-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqz-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 241 and 0 Target number of residues in the AU: 241 Target solvent content: 0.6411 Checking the provided sequence file Detected sequence length: 341 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 341 Adjusted target solvent content: 0.49 Input MTZ file: 1vqz-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: 19 Cell parameters: 45.503 70.280 113.629 90.000 90.000 90.000 Input sequence file: 1vqz-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2728 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: 59.771 3.800 Wilson plot Bfac: 71.94 3879 reflections ( 99.67 % complete ) and 0 restraints for refining 3033 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3366 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3037 (Rfree = 0.000) for 3033 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.53 Search for helices and strands: 0 residues in 0 chains, 3101 seeds are put forward Round 1: 121 peptides, 25 chains. Longest chain 8 peptides. Score 0.278 Round 2: 153 peptides, 26 chains. Longest chain 14 peptides. Score 0.408 Round 3: 182 peptides, 30 chains. Longest chain 13 peptides. Score 0.458 Round 4: 195 peptides, 30 chains. Longest chain 13 peptides. Score 0.509 Round 5: 207 peptides, 28 chains. Longest chain 21 peptides. Score 0.583 Taking the results from Round 5 Chains 28, Residues 179, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.67 % complete ) and 5698 restraints for refining 2467 atoms. 5010 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2564 (Rfree = 0.000) for 2467 atoms. Found 6 (13 requested) and removed 18 (6 requested) atoms. Cycle 2: After refmac, R = 0.2393 (Rfree = 0.000) for 2425 atoms. Found 10 (13 requested) and removed 16 (6 requested) atoms. Cycle 3: After refmac, R = 0.2129 (Rfree = 0.000) for 2405 atoms. Found 8 (13 requested) and removed 13 (6 requested) atoms. Cycle 4: After refmac, R = 0.1971 (Rfree = 0.000) for 2387 atoms. Found 5 (13 requested) and removed 9 (6 requested) atoms. Cycle 5: After refmac, R = 0.2008 (Rfree = 0.000) for 2379 atoms. Found 4 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.58 Search for helices and strands: 0 residues in 0 chains, 2467 seeds are put forward Round 1: 155 peptides, 30 chains. Longest chain 9 peptides. Score 0.340 Round 2: 179 peptides, 27 chains. Longest chain 14 peptides. Score 0.497 Round 3: 193 peptides, 29 chains. Longest chain 20 peptides. Score 0.517 Round 4: 196 peptides, 30 chains. Longest chain 15 peptides. Score 0.512 Round 5: 194 peptides, 25 chains. Longest chain 22 peptides. Score 0.584 Taking the results from Round 5 Chains 26, Residues 169, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.67 % complete ) and 5485 restraints for refining 2466 atoms. 4766 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2148 (Rfree = 0.000) for 2466 atoms. Found 6 (13 requested) and removed 10 (6 requested) atoms. Cycle 7: After refmac, R = 0.1993 (Rfree = 0.000) for 2449 atoms. Found 3 (13 requested) and removed 6 (6 requested) atoms. Cycle 8: After refmac, R = 0.2102 (Rfree = 0.000) for 2445 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 9: After refmac, R = 0.1986 (Rfree = 0.000) for 2440 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 10: After refmac, R = 0.1986 (Rfree = 0.000) for 2432 atoms. Found 12 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.59 Search for helices and strands: 0 residues in 0 chains, 2536 seeds are put forward Round 1: 143 peptides, 26 chains. Longest chain 11 peptides. Score 0.363 Round 2: 166 peptides, 27 chains. Longest chain 12 peptides. Score 0.445 Round 3: 176 peptides, 26 chains. Longest chain 12 peptides. Score 0.503 Round 4: 172 peptides, 25 chains. Longest chain 12 peptides. Score 0.504 Round 5: 175 peptides, 24 chains. Longest chain 16 peptides. Score 0.533 Taking the results from Round 5 Chains 24, Residues 151, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.67 % complete ) and 5804 restraints for refining 2467 atoms. 5224 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2344 (Rfree = 0.000) for 2467 atoms. Found 10 (13 requested) and removed 12 (6 requested) atoms. Cycle 12: After refmac, R = 0.2169 (Rfree = 0.000) for 2444 atoms. Found 12 (13 requested) and removed 10 (6 requested) atoms. Cycle 13: After refmac, R = 0.2127 (Rfree = 0.000) for 2431 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 14: After refmac, R = 0.1846 (Rfree = 0.000) for 2417 atoms. Found 8 (13 requested) and removed 6 (6 requested) atoms. Cycle 15: After refmac, R = 0.1734 (Rfree = 0.000) for 2414 atoms. Found 8 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 2502 seeds are put forward Round 1: 116 peptides, 23 chains. Longest chain 8 peptides. Score 0.295 Round 2: 138 peptides, 20 chains. Longest chain 12 peptides. Score 0.457 Round 3: 148 peptides, 21 chains. Longest chain 12 peptides. Score 0.480 Round 4: 153 peptides, 21 chains. Longest chain 14 peptides. Score 0.500 Round 5: 161 peptides, 25 chains. Longest chain 18 peptides. Score 0.460 Taking the results from Round 4 Chains 21, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.67 % complete ) and 5864 restraints for refining 2466 atoms. 5357 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2166 (Rfree = 0.000) for 2466 atoms. Found 8 (13 requested) and removed 11 (6 requested) atoms. Cycle 17: After refmac, R = 0.1993 (Rfree = 0.000) for 2457 atoms. Found 12 (13 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.2037 (Rfree = 0.000) for 2457 atoms. Found 9 (13 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.1921 (Rfree = 0.000) for 2456 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1572 (Rfree = 0.000) for 2460 atoms. Found 1 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.58 Search for helices and strands: 0 residues in 0 chains, 2524 seeds are put forward Round 1: 134 peptides, 25 chains. Longest chain 9 peptides. Score 0.341 Round 2: 162 peptides, 27 chains. Longest chain 12 peptides. Score 0.428 Round 3: 155 peptides, 24 chains. Longest chain 13 peptides. Score 0.454 Round 4: 158 peptides, 27 chains. Longest chain 11 peptides. Score 0.411 Round 5: 157 peptides, 24 chains. Longest chain 12 peptides. Score 0.462 Taking the results from Round 5 Chains 24, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.67 % complete ) and 5840 restraints for refining 2467 atoms. 5332 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2572 (Rfree = 0.000) for 2467 atoms. Found 13 (13 requested) and removed 103 (6 requested) atoms. Cycle 22: After refmac, R = 0.2567 (Rfree = 0.000) for 2361 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 23: After refmac, R = 0.2198 (Rfree = 0.000) for 2354 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 24: After refmac, R = 0.2106 (Rfree = 0.000) for 2351 atoms. Found 10 (12 requested) and removed 12 (6 requested) atoms. Cycle 25: After refmac, R = 0.2019 (Rfree = 0.000) for 2348 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.51 3.56 Search for helices and strands: 0 residues in 0 chains, 2415 seeds are put forward Round 1: 121 peptides, 23 chains. Longest chain 11 peptides. Score 0.320 Round 2: 139 peptides, 24 chains. Longest chain 14 peptides. Score 0.384 Round 3: 139 peptides, 24 chains. Longest chain 18 peptides. Score 0.384 Round 4: 143 peptides, 23 chains. Longest chain 22 peptides. Score 0.421 Round 5: 148 peptides, 25 chains. Longest chain 17 peptides. Score 0.405 Taking the results from Round 4 Chains 24, Residues 120, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.67 % complete ) and 5791 restraints for refining 2467 atoms. 5257 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2140 (Rfree = 0.000) for 2467 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 27: After refmac, R = 0.2142 (Rfree = 0.000) for 2457 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.1948 (Rfree = 0.000) for 2451 atoms. Found 8 (13 requested) and removed 11 (6 requested) atoms. Cycle 29: After refmac, R = 0.1908 (Rfree = 0.000) for 2442 atoms. Found 9 (13 requested) and removed 13 (6 requested) atoms. Cycle 30: After refmac, R = 0.1819 (Rfree = 0.000) for 2430 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 2499 seeds are put forward Round 1: 129 peptides, 28 chains. Longest chain 7 peptides. Score 0.256 Round 2: 147 peptides, 28 chains. Longest chain 14 peptides. Score 0.342 Round 3: 139 peptides, 26 chains. Longest chain 15 peptides. Score 0.345 Round 4: 150 peptides, 27 chains. Longest chain 14 peptides. Score 0.376 Round 5: 148 peptides, 25 chains. Longest chain 10 peptides. Score 0.405 Taking the results from Round 5 Chains 25, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.67 % complete ) and 5928 restraints for refining 2467 atoms. 5461 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1993 (Rfree = 0.000) for 2467 atoms. Found 8 (13 requested) and removed 187 (6 requested) atoms. Cycle 32: After refmac, R = 0.2112 (Rfree = 0.000) for 2278 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 33: After refmac, R = 0.2056 (Rfree = 0.000) for 2269 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 34: After refmac, R = 0.1871 (Rfree = 0.000) for 2267 atoms. Found 10 (12 requested) and removed 8 (6 requested) atoms. Cycle 35: After refmac, R = 0.1797 (Rfree = 0.000) for 2268 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.54 Search for helices and strands: 0 residues in 0 chains, 2376 seeds are put forward Round 1: 127 peptides, 26 chains. Longest chain 9 peptides. Score 0.287 Round 2: 135 peptides, 25 chains. Longest chain 10 peptides. Score 0.346 Round 3: 133 peptides, 27 chains. Longest chain 7 peptides. Score 0.296 Round 4: 126 peptides, 23 chains. Longest chain 12 peptides. Score 0.344 Round 5: 141 peptides, 25 chains. Longest chain 14 peptides. Score 0.374 Taking the results from Round 5 Chains 25, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.67 % complete ) and 5842 restraints for refining 2465 atoms. 5403 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1934 (Rfree = 0.000) for 2465 atoms. Found 9 (13 requested) and removed 18 (6 requested) atoms. Cycle 37: After refmac, R = 0.1771 (Rfree = 0.000) for 2450 atoms. Found 10 (13 requested) and removed 14 (6 requested) atoms. Cycle 38: After refmac, R = 0.1780 (Rfree = 0.000) for 2442 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.1668 (Rfree = 0.000) for 2441 atoms. Found 10 (13 requested) and removed 13 (6 requested) atoms. Cycle 40: After refmac, R = 0.2176 (Rfree = 0.000) for 2437 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.59 Search for helices and strands: 0 residues in 0 chains, 2528 seeds are put forward Round 1: 132 peptides, 28 chains. Longest chain 7 peptides. Score 0.270 Round 2: 142 peptides, 26 chains. Longest chain 12 peptides. Score 0.359 Round 3: 129 peptides, 25 chains. Longest chain 10 peptides. Score 0.317 Round 4: 142 peptides, 26 chains. Longest chain 12 peptides. Score 0.359 Round 5: 121 peptides, 21 chains. Longest chain 12 peptides. Score 0.361 Taking the results from Round 5 Chains 21, Residues 100, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3879 reflections ( 99.67 % complete ) and 6001 restraints for refining 2467 atoms. 5622 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1816 (Rfree = 0.000) for 2467 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 42: After refmac, R = 0.1673 (Rfree = 0.000) for 2464 atoms. Found 2 (13 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.1778 (Rfree = 0.000) for 2456 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. Cycle 44: After refmac, R = 0.1669 (Rfree = 0.000) for 2453 atoms. Found 7 (13 requested) and removed 9 (6 requested) atoms. Cycle 45: After refmac, R = 0.1732 (Rfree = 0.000) for 2448 atoms. Found 5 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.55 Search for helices and strands: 0 residues in 0 chains, 2508 seeds are put forward Round 1: 82 peptides, 19 chains. Longest chain 7 peptides. Score 0.203 Round 2: 112 peptides, 19 chains. Longest chain 10 peptides. Score 0.360 Round 3: 114 peptides, 20 chains. Longest chain 12 peptides. Score 0.349 Round 4: 118 peptides, 21 chains. Longest chain 9 peptides. Score 0.347 Round 5: 111 peptides, 18 chains. Longest chain 15 peptides. Score 0.376 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 93, 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 1vqz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3879 reflections ( 99.67 % complete ) and 6068 restraints for refining 2467 atoms. 5714 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1943 (Rfree = 0.000) for 2467 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.1936 (Rfree = 0.000) for 2453 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1768 (Rfree = 0.000) for 2445 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1743 (Rfree = 0.000) for 2437 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:08:57 GMT 2018 Job finished. TimeTaking 46.25 Used memory is bytes: 4426104