null Tue 25 Dec 19:27:55 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 1vlc-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlc-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-3.4-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/1vlc-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-3.4-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 19:28:05 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/1vlc-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlc-3.4-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 345 and 0 Target number of residues in the AU: 345 Target solvent content: 0.6031 Checking the provided sequence file Detected sequence length: 366 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 366 Adjusted target solvent content: 0.58 Input MTZ file: 1vlc-3.4-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: 150 Cell parameters: 119.541 119.541 57.022 90.000 90.000 120.000 Input sequence file: 1vlc-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2928 target number of atoms Had to go as low as 0.90 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: 103.526 3.400 Wilson plot Bfac: 53.74 6661 reflections ( 99.76 % complete ) and 0 restraints for refining 3292 atoms. Observations/parameters ratio is 0.51 ------------------------------------------------------ Starting model: R = 0.3172 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2995 (Rfree = 0.000) for 3292 atoms. Found 24 (24 requested) and removed 23 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.17 2.85 Search for helices and strands: 0 residues in 0 chains, 3370 seeds are put forward Round 1: 190 peptides, 34 chains. Longest chain 14 peptides. Score 0.375 Round 2: 226 peptides, 35 chains. Longest chain 16 peptides. Score 0.479 Round 3: 232 peptides, 33 chains. Longest chain 19 peptides. Score 0.523 Round 4: 252 peptides, 31 chains. Longest chain 30 peptides. Score 0.602 Round 5: 244 peptides, 28 chains. Longest chain 26 peptides. Score 0.616 Taking the results from Round 5 Chains 31, Residues 216, Estimated correctness of the model 33.8 % 5 chains (56 residues) have been docked in sequence ------------------------------------------------------ 6661 reflections ( 99.76 % complete ) and 5151 restraints for refining 2662 atoms. 4116 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2505 (Rfree = 0.000) for 2662 atoms. Found 20 (20 requested) and removed 27 (10 requested) atoms. Cycle 2: After refmac, R = 0.2336 (Rfree = 0.000) for 2627 atoms. Found 18 (20 requested) and removed 18 (10 requested) atoms. Cycle 3: After refmac, R = 0.2316 (Rfree = 0.000) for 2616 atoms. Found 17 (19 requested) and removed 12 (9 requested) atoms. Cycle 4: After refmac, R = 0.2174 (Rfree = 0.000) for 2614 atoms. Found 5 (19 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.2190 (Rfree = 0.000) for 2604 atoms. Found 13 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 2.75 Search for helices and strands: 0 residues in 0 chains, 2712 seeds are put forward Round 1: 245 peptides, 34 chains. Longest chain 24 peptides. Score 0.548 Round 2: 257 peptides, 29 chains. Longest chain 22 peptides. Score 0.636 Round 3: 255 peptides, 29 chains. Longest chain 25 peptides. Score 0.632 Round 4: 246 peptides, 22 chains. Longest chain 33 peptides. Score 0.686 Round 5: 257 peptides, 24 chains. Longest chain 23 peptides. Score 0.689 Taking the results from Round 5 Chains 26, Residues 233, Estimated correctness of the model 55.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6661 reflections ( 99.76 % complete ) and 5569 restraints for refining 2663 atoms. 4624 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2407 (Rfree = 0.000) for 2663 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 7: After refmac, R = 0.2193 (Rfree = 0.000) for 2658 atoms. Found 12 (20 requested) and removed 11 (10 requested) atoms. Cycle 8: After refmac, R = 0.2085 (Rfree = 0.000) for 2653 atoms. Found 1 (20 requested) and removed 14 (10 requested) atoms. Cycle 9: After refmac, R = 0.2097 (Rfree = 0.000) for 2639 atoms. Found 9 (19 requested) and removed 10 (9 requested) atoms. Cycle 10: After refmac, R = 0.2028 (Rfree = 0.000) for 2636 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 2.83 Search for helices and strands: 0 residues in 0 chains, 2733 seeds are put forward Round 1: 248 peptides, 32 chains. Longest chain 21 peptides. Score 0.580 Round 2: 247 peptides, 25 chains. Longest chain 20 peptides. Score 0.656 Round 3: 270 peptides, 28 chains. Longest chain 24 peptides. Score 0.676 Round 4: 263 peptides, 26 chains. Longest chain 22 peptides. Score 0.681 Round 5: 269 peptides, 29 chains. Longest chain 26 peptides. Score 0.664 Taking the results from Round 4 Chains 26, Residues 237, Estimated correctness of the model 52.9 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6661 reflections ( 99.76 % complete ) and 5644 restraints for refining 2662 atoms. 4638 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2409 (Rfree = 0.000) for 2662 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 12: After refmac, R = 0.2132 (Rfree = 0.000) for 2657 atoms. Found 6 (20 requested) and removed 15 (10 requested) atoms. Cycle 13: After refmac, R = 0.2010 (Rfree = 0.000) for 2642 atoms. Found 8 (19 requested) and removed 13 (9 requested) atoms. Cycle 14: After refmac, R = 0.1958 (Rfree = 0.000) for 2628 atoms. Found 7 (19 requested) and removed 10 (9 requested) atoms. Cycle 15: After refmac, R = 0.1995 (Rfree = 0.000) for 2623 atoms. Found 10 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 2727 seeds are put forward Round 1: 238 peptides, 28 chains. Longest chain 18 peptides. Score 0.601 Round 2: 240 peptides, 25 chains. Longest chain 22 peptides. Score 0.640 Round 3: 239 peptides, 24 chains. Longest chain 22 peptides. Score 0.649 Round 4: 247 peptides, 26 chains. Longest chain 36 peptides. Score 0.646 Round 5: 253 peptides, 26 chains. Longest chain 24 peptides. Score 0.659 Taking the results from Round 5 Chains 27, Residues 227, Estimated correctness of the model 46.7 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 6661 reflections ( 99.76 % complete ) and 5624 restraints for refining 2663 atoms. 4646 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2398 (Rfree = 0.000) for 2663 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 17: After refmac, R = 0.2274 (Rfree = 0.000) for 2649 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 18: After refmac, R = 0.2202 (Rfree = 0.000) for 2650 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 19: After refmac, R = 0.2094 (Rfree = 0.000) for 2643 atoms. Found 19 (20 requested) and removed 12 (10 requested) atoms. Cycle 20: After refmac, R = 0.2076 (Rfree = 0.000) for 2649 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 2.80 Search for helices and strands: 0 residues in 0 chains, 2756 seeds are put forward Round 1: 239 peptides, 36 chains. Longest chain 20 peptides. Score 0.505 Round 2: 256 peptides, 26 chains. Longest chain 25 peptides. Score 0.666 Round 3: 256 peptides, 26 chains. Longest chain 23 peptides. Score 0.666 Round 4: 244 peptides, 25 chains. Longest chain 25 peptides. Score 0.650 Round 5: 260 peptides, 28 chains. Longest chain 23 peptides. Score 0.654 Taking the results from Round 3 Chains 28, Residues 230, Estimated correctness of the model 48.7 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 6661 reflections ( 99.76 % complete ) and 5276 restraints for refining 2663 atoms. 4215 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2375 (Rfree = 0.000) for 2663 atoms. Found 20 (20 requested) and removed 16 (10 requested) atoms. Cycle 22: After refmac, R = 0.2183 (Rfree = 0.000) for 2652 atoms. Found 7 (20 requested) and removed 14 (10 requested) atoms. Cycle 23: After refmac, R = 0.2088 (Rfree = 0.000) for 2639 atoms. Found 2 (19 requested) and removed 11 (9 requested) atoms. Cycle 24: After refmac, R = 0.2076 (Rfree = 0.000) for 2624 atoms. Found 7 (19 requested) and removed 9 (9 requested) atoms. Cycle 25: After refmac, R = 0.2001 (Rfree = 0.000) for 2619 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 2.85 Search for helices and strands: 0 residues in 0 chains, 2726 seeds are put forward Round 1: 227 peptides, 29 chains. Longest chain 19 peptides. Score 0.560 Round 2: 238 peptides, 27 chains. Longest chain 18 peptides. Score 0.613 Round 3: 240 peptides, 30 chains. Longest chain 29 peptides. Score 0.583 Round 4: 246 peptides, 26 chains. Longest chain 24 peptides. Score 0.643 Round 5: 232 peptides, 23 chains. Longest chain 27 peptides. Score 0.643 Taking the results from Round 5 Chains 25, Residues 209, Estimated correctness of the model 42.1 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 6661 reflections ( 99.76 % complete ) and 5774 restraints for refining 2662 atoms. 4910 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2368 (Rfree = 0.000) for 2662 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. Cycle 27: After refmac, R = 0.2068 (Rfree = 0.000) for 2655 atoms. Found 12 (20 requested) and removed 11 (10 requested) atoms. Cycle 28: After refmac, R = 0.2017 (Rfree = 0.000) for 2646 atoms. Found 15 (20 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.2013 (Rfree = 0.000) for 2639 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 30: After refmac, R = 0.1951 (Rfree = 0.000) for 2638 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.11 2.79 Search for helices and strands: 0 residues in 0 chains, 2754 seeds are put forward Round 1: 229 peptides, 31 chains. Longest chain 17 peptides. Score 0.540 Round 2: 244 peptides, 30 chains. Longest chain 18 peptides. Score 0.593 Round 3: 230 peptides, 26 chains. Longest chain 17 peptides. Score 0.604 Round 4: 238 peptides, 27 chains. Longest chain 19 peptides. Score 0.613 Round 5: 253 peptides, 29 chains. Longest chain 19 peptides. Score 0.627 Taking the results from Round 5 Chains 31, Residues 224, Estimated correctness of the model 37.2 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6661 reflections ( 99.76 % complete ) and 5551 restraints for refining 2663 atoms. 4610 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2288 (Rfree = 0.000) for 2663 atoms. Found 20 (20 requested) and removed 15 (10 requested) atoms. Cycle 32: After refmac, R = 0.2118 (Rfree = 0.000) for 2653 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.1991 (Rfree = 0.000) for 2659 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 34: After refmac, R = 0.1829 (Rfree = 0.000) for 2659 atoms. Found 9 (20 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1807 (Rfree = 0.000) for 2654 atoms. Found 10 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 2.78 Search for helices and strands: 0 residues in 0 chains, 2759 seeds are put forward Round 1: 215 peptides, 34 chains. Longest chain 12 peptides. Score 0.458 Round 2: 255 peptides, 30 chains. Longest chain 24 peptides. Score 0.621 Round 3: 255 peptides, 28 chains. Longest chain 20 peptides. Score 0.643 Round 4: 243 peptides, 28 chains. Longest chain 20 peptides. Score 0.614 Round 5: 255 peptides, 31 chains. Longest chain 20 peptides. Score 0.609 Taking the results from Round 3 Chains 28, Residues 227, Estimated correctness of the model 42.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6661 reflections ( 99.76 % complete ) and 5707 restraints for refining 2663 atoms. 4827 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2027 (Rfree = 0.000) for 2663 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 37: After refmac, R = 0.1922 (Rfree = 0.000) for 2668 atoms. Found 11 (20 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.1840 (Rfree = 0.000) for 2663 atoms. Found 12 (20 requested) and removed 14 (10 requested) atoms. Cycle 39: After refmac, R = 0.1790 (Rfree = 0.000) for 2654 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 40: After refmac, R = 0.1750 (Rfree = 0.000) for 2654 atoms. Found 7 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 2.84 Search for helices and strands: 0 residues in 0 chains, 2747 seeds are put forward Round 1: 207 peptides, 36 chains. Longest chain 16 peptides. Score 0.404 Round 2: 234 peptides, 31 chains. Longest chain 16 peptides. Score 0.554 Round 3: 225 peptides, 27 chains. Longest chain 21 peptides. Score 0.579 Round 4: 231 peptides, 30 chains. Longest chain 18 peptides. Score 0.558 Round 5: 237 peptides, 31 chains. Longest chain 17 peptides. Score 0.563 Taking the results from Round 3 Chains 28, Residues 198, Estimated correctness of the model 21.7 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6661 reflections ( 99.76 % complete ) and 5867 restraints for refining 2663 atoms. 5073 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1985 (Rfree = 0.000) for 2663 atoms. Found 19 (20 requested) and removed 11 (10 requested) atoms. Cycle 42: After refmac, R = 0.1871 (Rfree = 0.000) for 2655 atoms. Found 18 (20 requested) and removed 10 (10 requested) atoms. Cycle 43: After refmac, R = 0.1812 (Rfree = 0.000) for 2656 atoms. Found 18 (20 requested) and removed 11 (10 requested) atoms. Cycle 44: After refmac, R = 0.1745 (Rfree = 0.000) for 2660 atoms. Found 12 (20 requested) and removed 11 (10 requested) atoms. Cycle 45: After refmac, R = 0.1766 (Rfree = 0.000) for 2656 atoms. Found 15 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.11 2.79 Search for helices and strands: 0 residues in 0 chains, 2777 seeds are put forward Round 1: 215 peptides, 36 chains. Longest chain 14 peptides. Score 0.431 Round 2: 235 peptides, 29 chains. Longest chain 22 peptides. Score 0.581 Round 3: 229 peptides, 32 chains. Longest chain 24 peptides. Score 0.528 Round 4: 246 peptides, 30 chains. Longest chain 16 peptides. Score 0.598 Round 5: 230 peptides, 31 chains. Longest chain 19 peptides. Score 0.543 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 216, Estimated correctness of the model 28.0 % 3 chains (30 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 1vlc-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 278 A and 292 A 28 chains (223 residues) following loop building 2 chains (43 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6661 reflections ( 99.76 % complete ) and 5418 restraints for refining 2662 atoms. 4445 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2220 (Rfree = 0.000) for 2662 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 47: After refmac, R = 0.2130 (Rfree = 0.000) for 2645 atoms. Found 0 (20 requested) and removed 10 (10 requested) atoms. Cycle 48: After refmac, R = 0.2045 (Rfree = 0.000) for 2625 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1985 (Rfree = 0.000) for 2609 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:28:28 GMT 2018 Job finished. TimeTaking 60.55 Used memory is bytes: 5792200