null 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 1vli-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vli-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vli-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-4.0-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/1vli-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-4.0-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 19:28:06 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/1vli-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vli-4.0-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 343 and 0 Target number of residues in the AU: 343 Target solvent content: 0.6861 Checking the provided sequence file Detected sequence length: 385 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 385 Adjusted target solvent content: 0.65 Input MTZ file: 1vli-4.0-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: 154 Cell parameters: 70.614 70.614 205.438 90.000 90.000 120.000 Input sequence file: 1vli-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3080 target number of atoms Had to go as low as 1.10 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: 68.479 4.000 Wilson plot Bfac: 106.94 5431 reflections ( 99.58 % complete ) and 0 restraints for refining 3421 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3792 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3320 (Rfree = 0.000) for 3421 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.00 3.25 Search for helices and strands: 0 residues in 0 chains, 3478 seeds are put forward Round 1: 162 peptides, 26 chains. Longest chain 12 peptides. Score 0.365 Round 2: 202 peptides, 23 chains. Longest chain 21 peptides. Score 0.511 Round 3: 207 peptides, 24 chains. Longest chain 21 peptides. Score 0.511 Round 4: 206 peptides, 24 chains. Longest chain 17 peptides. Score 0.509 Round 5: 219 peptides, 29 chains. Longest chain 19 peptides. Score 0.484 Taking the results from Round 3 Chains 25, Residues 183, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 5431 reflections ( 99.58 % complete ) and 6416 restraints for refining 2778 atoms. 5665 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2908 (Rfree = 0.000) for 2778 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 2: After refmac, R = 0.2814 (Rfree = 0.000) for 2733 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.2746 (Rfree = 0.000) for 2713 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 4: After refmac, R = 0.2551 (Rfree = 0.000) for 2680 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 5: After refmac, R = 0.2438 (Rfree = 0.000) for 2664 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.99 3.25 Search for helices and strands: 0 residues in 0 chains, 2787 seeds are put forward Round 1: 202 peptides, 32 chains. Longest chain 15 peptides. Score 0.403 Round 2: 212 peptides, 25 chains. Longest chain 20 peptides. Score 0.512 Round 3: 218 peptides, 23 chains. Longest chain 19 peptides. Score 0.549 Round 4: 217 peptides, 21 chains. Longest chain 34 peptides. Score 0.568 Round 5: 214 peptides, 24 chains. Longest chain 27 peptides. Score 0.528 Taking the results from Round 4 Chains 23, Residues 196, Estimated correctness of the model 0.0 % 4 chains (55 residues) have been docked in sequence ------------------------------------------------------ 5431 reflections ( 99.58 % complete ) and 5733 restraints for refining 2781 atoms. 4774 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2851 (Rfree = 0.000) for 2781 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 7: After refmac, R = 0.2659 (Rfree = 0.000) for 2734 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 8: After refmac, R = 0.2412 (Rfree = 0.000) for 2690 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 9: After refmac, R = 0.2526 (Rfree = 0.000) for 2659 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 10: After refmac, R = 0.2350 (Rfree = 0.000) for 2638 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.89 3.17 Search for helices and strands: 0 residues in 0 chains, 2740 seeds are put forward Round 1: 194 peptides, 28 chains. Longest chain 17 peptides. Score 0.430 Round 2: 218 peptides, 25 chains. Longest chain 21 peptides. Score 0.527 Round 3: 214 peptides, 24 chains. Longest chain 27 peptides. Score 0.528 Round 4: 203 peptides, 22 chains. Longest chain 22 peptides. Score 0.525 Round 5: 206 peptides, 22 chains. Longest chain 25 peptides. Score 0.532 Taking the results from Round 5 Chains 23, Residues 184, Estimated correctness of the model 0.0 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 5431 reflections ( 99.58 % complete ) and 6213 restraints for refining 2781 atoms. 5414 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2914 (Rfree = 0.000) for 2781 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 12: After refmac, R = 0.2850 (Rfree = 0.000) for 2729 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 13: After refmac, R = 0.2487 (Rfree = 0.000) for 2683 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2496 (Rfree = 0.000) for 2670 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 15: After refmac, R = 0.2381 (Rfree = 0.000) for 2656 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.97 3.23 Search for helices and strands: 0 residues in 0 chains, 2777 seeds are put forward Round 1: 184 peptides, 26 chains. Longest chain 17 peptides. Score 0.428 Round 2: 200 peptides, 22 chains. Longest chain 19 peptides. Score 0.517 Round 3: 221 peptides, 26 chains. Longest chain 19 peptides. Score 0.523 Round 4: 225 peptides, 29 chains. Longest chain 26 peptides. Score 0.499 Round 5: 224 peptides, 22 chains. Longest chain 18 peptides. Score 0.573 Taking the results from Round 5 Chains 22, Residues 202, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5431 reflections ( 99.58 % complete ) and 6529 restraints for refining 2781 atoms. 5743 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2446 (Rfree = 0.000) for 2781 atoms. Found 12 (13 requested) and removed 7 (6 requested) atoms. Cycle 17: After refmac, R = 0.2200 (Rfree = 0.000) for 2751 atoms. Found 9 (13 requested) and removed 11 (6 requested) atoms. Cycle 18: After refmac, R = 0.2150 (Rfree = 0.000) for 2733 atoms. Found 10 (13 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.2035 (Rfree = 0.000) for 2725 atoms. Found 11 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.2026 (Rfree = 0.000) for 2711 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.91 3.18 Search for helices and strands: 0 residues in 0 chains, 2826 seeds are put forward Round 1: 185 peptides, 28 chains. Longest chain 13 peptides. Score 0.405 Round 2: 205 peptides, 23 chains. Longest chain 16 peptides. Score 0.518 Round 3: 216 peptides, 25 chains. Longest chain 31 peptides. Score 0.522 Round 4: 205 peptides, 25 chains. Longest chain 25 peptides. Score 0.495 Round 5: 207 peptides, 25 chains. Longest chain 25 peptides. Score 0.500 Taking the results from Round 3 Chains 25, Residues 191, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5431 reflections ( 99.58 % complete ) and 6365 restraints for refining 2781 atoms. 5626 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2247 (Rfree = 0.000) for 2781 atoms. Found 11 (13 requested) and removed 8 (6 requested) atoms. Cycle 22: After refmac, R = 0.2094 (Rfree = 0.000) for 2752 atoms. Found 11 (13 requested) and removed 10 (6 requested) atoms. Cycle 23: After refmac, R = 0.2193 (Rfree = 0.000) for 2739 atoms. Found 9 (13 requested) and removed 10 (6 requested) atoms. Cycle 24: After refmac, R = 0.2131 (Rfree = 0.000) for 2721 atoms. Found 5 (13 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.2078 (Rfree = 0.000) for 2707 atoms. Found 8 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.95 3.21 Search for helices and strands: 0 residues in 0 chains, 2847 seeds are put forward Round 1: 160 peptides, 27 chains. Longest chain 16 peptides. Score 0.345 Round 2: 178 peptides, 23 chains. Longest chain 18 peptides. Score 0.449 Round 3: 186 peptides, 25 chains. Longest chain 20 peptides. Score 0.446 Round 4: 198 peptides, 26 chains. Longest chain 21 peptides. Score 0.465 Round 5: 198 peptides, 26 chains. Longest chain 23 peptides. Score 0.465 Taking the results from Round 5 Chains 26, Residues 172, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5431 reflections ( 99.58 % complete ) and 6261 restraints for refining 2780 atoms. 5558 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2320 (Rfree = 0.000) for 2780 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 27: After refmac, R = 0.2165 (Rfree = 0.000) for 2748 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.2209 (Rfree = 0.000) for 2736 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 29: After refmac, R = 0.2155 (Rfree = 0.000) for 2722 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 30: After refmac, R = 0.2129 (Rfree = 0.000) for 2707 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.91 3.18 Search for helices and strands: 0 residues in 0 chains, 2811 seeds are put forward Round 1: 164 peptides, 29 chains. Longest chain 10 peptides. Score 0.331 Round 2: 190 peptides, 29 chains. Longest chain 12 peptides. Score 0.407 Round 3: 189 peptides, 26 chains. Longest chain 24 peptides. Score 0.441 Round 4: 202 peptides, 24 chains. Longest chain 22 peptides. Score 0.499 Round 5: 206 peptides, 23 chains. Longest chain 28 peptides. Score 0.520 Taking the results from Round 5 Chains 26, Residues 183, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5431 reflections ( 99.58 % complete ) and 6129 restraints for refining 2781 atoms. 5325 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2421 (Rfree = 0.000) for 2781 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. Cycle 32: After refmac, R = 0.2298 (Rfree = 0.000) for 2734 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 33: After refmac, R = 0.2248 (Rfree = 0.000) for 2714 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 34: After refmac, R = 0.2147 (Rfree = 0.000) for 2695 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 35: After refmac, R = 0.2138 (Rfree = 0.000) for 2690 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.89 3.17 Search for helices and strands: 0 residues in 0 chains, 2829 seeds are put forward Round 1: 175 peptides, 30 chains. Longest chain 12 peptides. Score 0.351 Round 2: 187 peptides, 27 chains. Longest chain 13 peptides. Score 0.423 Round 3: 197 peptides, 28 chains. Longest chain 18 peptides. Score 0.438 Round 4: 192 peptides, 25 chains. Longest chain 20 peptides. Score 0.462 Round 5: 197 peptides, 26 chains. Longest chain 18 peptides. Score 0.463 Taking the results from Round 5 Chains 26, Residues 171, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5431 reflections ( 99.58 % complete ) and 6380 restraints for refining 2781 atoms. 5685 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2436 (Rfree = 0.000) for 2781 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 37: After refmac, R = 0.2252 (Rfree = 0.000) for 2747 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. Cycle 38: After refmac, R = 0.2358 (Rfree = 0.000) for 2732 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 39: After refmac, R = 0.2169 (Rfree = 0.000) for 2716 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 40: After refmac, R = 0.2223 (Rfree = 0.000) for 2709 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.88 3.16 Search for helices and strands: 0 residues in 0 chains, 2844 seeds are put forward Round 1: 171 peptides, 33 chains. Longest chain 11 peptides. Score 0.299 Round 2: 164 peptides, 27 chains. Longest chain 9 peptides. Score 0.357 Round 3: 174 peptides, 24 chains. Longest chain 21 peptides. Score 0.426 Round 4: 171 peptides, 26 chains. Longest chain 16 peptides. Score 0.391 Round 5: 203 peptides, 27 chains. Longest chain 13 peptides. Score 0.466 Taking the results from Round 5 Chains 27, Residues 176, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5431 reflections ( 99.58 % complete ) and 6463 restraints for refining 2781 atoms. 5772 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2682 (Rfree = 0.000) for 2781 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 42: After refmac, R = 0.2510 (Rfree = 0.000) for 2757 atoms. Found 13 (13 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.2335 (Rfree = 0.000) for 2749 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 44: After refmac, R = 0.2340 (Rfree = 0.000) for 2737 atoms. Found 13 (13 requested) and removed 8 (6 requested) atoms. Cycle 45: After refmac, R = 0.2223 (Rfree = 0.000) for 2725 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.92 3.19 Search for helices and strands: 0 residues in 0 chains, 2852 seeds are put forward Round 1: 155 peptides, 30 chains. Longest chain 11 peptides. Score 0.289 Round 2: 166 peptides, 26 chains. Longest chain 13 peptides. Score 0.377 Round 3: 169 peptides, 25 chains. Longest chain 18 peptides. Score 0.399 Round 4: 163 peptides, 24 chains. Longest chain 14 peptides. Score 0.394 Round 5: 167 peptides, 25 chains. Longest chain 16 peptides. Score 0.393 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 144, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vli-4_warpNtrace.pdb as input Building loops using Loopy2018 25 chains (144 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5431 reflections ( 99.58 % complete ) and 6443 restraints for refining 2755 atoms. 5876 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2542 (Rfree = 0.000) for 2755 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2384 (Rfree = 0.000) for 2727 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2219 (Rfree = 0.000) for 2705 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2271 (Rfree = 0.000) for 2683 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:25:02 GMT 2018 Job finished. TimeTaking 57.09 Used memory is bytes: 4821768