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 1vra-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vra-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vra-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-3.6-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/1vra-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-3.6-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/1vra-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vra-3.6-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 399 and 0 Target number of residues in the AU: 399 Target solvent content: 0.6109 Checking the provided sequence file Detected sequence length: 423 Maximum limit of NCS related copies: 30 Number of NCS-related molecules: 1 Adjusted target number of residues: 423 Adjusted target solvent content: 0.59 Input MTZ file: 1vra-3.6-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: 92 Cell parameters: 70.658 70.658 222.292 90.000 90.000 90.000 Input sequence file: 1vra-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3384 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: 29.814 3.600 Wilson plot Bfac: 57.13 7067 reflections ( 99.66 % complete ) and 0 restraints for refining 3723 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3698 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3645 (Rfree = 0.000) for 3723 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 2.83 Search for helices and strands: 0 residues in 0 chains, 3810 seeds are put forward Round 1: 199 peptides, 39 chains. Longest chain 11 peptides. Score 0.313 Round 2: 250 peptides, 34 chains. Longest chain 22 peptides. Score 0.519 Round 3: 268 peptides, 35 chains. Longest chain 20 peptides. Score 0.552 Round 4: 272 peptides, 34 chains. Longest chain 35 peptides. Score 0.572 Round 5: 275 peptides, 37 chains. Longest chain 23 peptides. Score 0.548 Taking the results from Round 4 Chains 36, Residues 238, Estimated correctness of the model 3.4 % 4 chains (66 residues) have been docked in sequence ------------------------------------------------------ 7067 reflections ( 99.66 % complete ) and 6192 restraints for refining 3068 atoms. 5056 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3189 (Rfree = 0.000) for 3068 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 2: After refmac, R = 0.2977 (Rfree = 0.000) for 2990 atoms. Found 18 (19 requested) and removed 28 (9 requested) atoms. Cycle 3: After refmac, R = 0.2824 (Rfree = 0.000) for 2951 atoms. Found 17 (19 requested) and removed 29 (9 requested) atoms. Cycle 4: After refmac, R = 0.2716 (Rfree = 0.000) for 2930 atoms. Found 18 (18 requested) and removed 28 (9 requested) atoms. Cycle 5: After refmac, R = 0.2563 (Rfree = 0.000) for 2910 atoms. Found 10 (18 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 2.78 Search for helices and strands: 0 residues in 0 chains, 3014 seeds are put forward Round 1: 251 peptides, 41 chains. Longest chain 17 peptides. Score 0.441 Round 2: 255 peptides, 38 chains. Longest chain 23 peptides. Score 0.487 Round 3: 267 peptides, 35 chains. Longest chain 21 peptides. Score 0.550 Round 4: 278 peptides, 36 chains. Longest chain 28 peptides. Score 0.565 Round 5: 289 peptides, 35 chains. Longest chain 23 peptides. Score 0.600 Taking the results from Round 5 Chains 38, Residues 254, Estimated correctness of the model 14.7 % 4 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7067 reflections ( 99.66 % complete ) and 6308 restraints for refining 3068 atoms. 5222 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3105 (Rfree = 0.000) for 3068 atoms. Found 19 (19 requested) and removed 42 (9 requested) atoms. Cycle 7: After refmac, R = 0.2770 (Rfree = 0.000) for 3004 atoms. Found 13 (19 requested) and removed 21 (9 requested) atoms. Cycle 8: After refmac, R = 0.2686 (Rfree = 0.000) for 2979 atoms. Found 9 (19 requested) and removed 24 (9 requested) atoms. Cycle 9: After refmac, R = 0.2640 (Rfree = 0.000) for 2949 atoms. Found 13 (19 requested) and removed 14 (9 requested) atoms. Cycle 10: After refmac, R = 0.2595 (Rfree = 0.000) for 2941 atoms. Found 9 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.15 2.79 Search for helices and strands: 0 residues in 0 chains, 3031 seeds are put forward Round 1: 234 peptides, 37 chains. Longest chain 14 peptides. Score 0.442 Round 2: 254 peptides, 34 chains. Longest chain 20 peptides. Score 0.529 Round 3: 282 peptides, 35 chains. Longest chain 21 peptides. Score 0.584 Round 4: 275 peptides, 38 chains. Longest chain 30 peptides. Score 0.537 Round 5: 260 peptides, 38 chains. Longest chain 22 peptides. Score 0.500 Taking the results from Round 3 Chains 38, Residues 247, Estimated correctness of the model 8.3 % 6 chains (45 residues) have been docked in sequence ------------------------------------------------------ 7067 reflections ( 99.66 % complete ) and 6185 restraints for refining 3068 atoms. 5110 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2834 (Rfree = 0.000) for 3068 atoms. Found 16 (19 requested) and removed 38 (9 requested) atoms. Cycle 12: After refmac, R = 0.2772 (Rfree = 0.000) for 3032 atoms. Found 14 (19 requested) and removed 25 (9 requested) atoms. Cycle 13: After refmac, R = 0.2629 (Rfree = 0.000) for 3009 atoms. Found 15 (19 requested) and removed 24 (9 requested) atoms. Cycle 14: After refmac, R = 0.2564 (Rfree = 0.000) for 2995 atoms. Found 14 (19 requested) and removed 22 (9 requested) atoms. Cycle 15: After refmac, R = 0.2549 (Rfree = 0.000) for 2986 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 2.79 Search for helices and strands: 0 residues in 0 chains, 3144 seeds are put forward Round 1: 253 peptides, 44 chains. Longest chain 14 peptides. Score 0.411 Round 2: 267 peptides, 41 chains. Longest chain 15 peptides. Score 0.484 Round 3: 263 peptides, 38 chains. Longest chain 18 peptides. Score 0.507 Round 4: 260 peptides, 35 chains. Longest chain 31 peptides. Score 0.533 Round 5: 265 peptides, 33 chains. Longest chain 35 peptides. Score 0.566 Taking the results from Round 5 Chains 37, Residues 232, Estimated correctness of the model 0.9 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 7067 reflections ( 99.66 % complete ) and 6284 restraints for refining 3066 atoms. 5267 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2957 (Rfree = 0.000) for 3066 atoms. Found 19 (19 requested) and removed 45 (9 requested) atoms. Cycle 17: After refmac, R = 0.2833 (Rfree = 0.000) for 3014 atoms. Found 17 (19 requested) and removed 24 (9 requested) atoms. Cycle 18: After refmac, R = 0.2648 (Rfree = 0.000) for 2998 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 19: After refmac, R = 0.2613 (Rfree = 0.000) for 2989 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 20: After refmac, R = 0.2448 (Rfree = 0.000) for 2967 atoms. Found 12 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.11 2.76 Search for helices and strands: 0 residues in 0 chains, 3090 seeds are put forward Round 1: 234 peptides, 37 chains. Longest chain 21 peptides. Score 0.442 Round 2: 243 peptides, 33 chains. Longest chain 16 peptides. Score 0.513 Round 3: 262 peptides, 35 chains. Longest chain 17 peptides. Score 0.538 Round 4: 235 peptides, 35 chains. Longest chain 24 peptides. Score 0.469 Round 5: 252 peptides, 32 chains. Longest chain 22 peptides. Score 0.546 Taking the results from Round 5 Chains 34, Residues 220, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7067 reflections ( 99.66 % complete ) and 6597 restraints for refining 3067 atoms. 5694 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2852 (Rfree = 0.000) for 3067 atoms. Found 17 (19 requested) and removed 35 (9 requested) atoms. Cycle 22: After refmac, R = 0.2709 (Rfree = 0.000) for 3030 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 23: After refmac, R = 0.2585 (Rfree = 0.000) for 3019 atoms. Found 17 (19 requested) and removed 26 (9 requested) atoms. Cycle 24: After refmac, R = 0.2402 (Rfree = 0.000) for 3006 atoms. Found 11 (19 requested) and removed 25 (9 requested) atoms. Cycle 25: After refmac, R = 0.2324 (Rfree = 0.000) for 2984 atoms. Found 16 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.18 2.82 Search for helices and strands: 0 residues in 0 chains, 3105 seeds are put forward Round 1: 224 peptides, 39 chains. Longest chain 16 peptides. Score 0.389 Round 2: 247 peptides, 34 chains. Longest chain 23 peptides. Score 0.512 Round 3: 258 peptides, 41 chains. Longest chain 16 peptides. Score 0.460 Round 4: 260 peptides, 34 chains. Longest chain 21 peptides. Score 0.544 Round 5: 250 peptides, 32 chains. Longest chain 24 peptides. Score 0.542 Taking the results from Round 4 Chains 36, Residues 226, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7067 reflections ( 99.66 % complete ) and 6452 restraints for refining 3067 atoms. 5514 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2808 (Rfree = 0.000) for 3067 atoms. Found 18 (19 requested) and removed 20 (9 requested) atoms. Cycle 27: After refmac, R = 0.2754 (Rfree = 0.000) for 3046 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 28: After refmac, R = 0.2642 (Rfree = 0.000) for 3033 atoms. Found 14 (19 requested) and removed 13 (9 requested) atoms. Cycle 29: After refmac, R = 0.2534 (Rfree = 0.000) for 3027 atoms. Found 11 (19 requested) and removed 22 (9 requested) atoms. Cycle 30: After refmac, R = 0.2522 (Rfree = 0.000) for 3012 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 2.80 Search for helices and strands: 0 residues in 0 chains, 3121 seeds are put forward Round 1: 207 peptides, 36 chains. Longest chain 15 peptides. Score 0.377 Round 2: 231 peptides, 33 chains. Longest chain 22 peptides. Score 0.482 Round 3: 233 peptides, 33 chains. Longest chain 21 peptides. Score 0.487 Round 4: 234 peptides, 33 chains. Longest chain 22 peptides. Score 0.490 Round 5: 232 peptides, 34 chains. Longest chain 21 peptides. Score 0.473 Taking the results from Round 4 Chains 34, Residues 201, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 7067 reflections ( 99.66 % complete ) and 6611 restraints for refining 3068 atoms. 5747 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2741 (Rfree = 0.000) for 3068 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 32: After refmac, R = 0.2581 (Rfree = 0.000) for 3053 atoms. Found 18 (19 requested) and removed 16 (9 requested) atoms. Cycle 33: After refmac, R = 0.2542 (Rfree = 0.000) for 3046 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 34: After refmac, R = 0.2478 (Rfree = 0.000) for 3042 atoms. Found 17 (19 requested) and removed 19 (9 requested) atoms. Cycle 35: After refmac, R = 0.2455 (Rfree = 0.000) for 3038 atoms. Found 15 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 2.82 Search for helices and strands: 0 residues in 0 chains, 3153 seeds are put forward Round 1: 203 peptides, 37 chains. Longest chain 15 peptides. Score 0.352 Round 2: 253 peptides, 36 chains. Longest chain 20 peptides. Score 0.504 Round 3: 243 peptides, 34 chains. Longest chain 24 peptides. Score 0.502 Round 4: 247 peptides, 36 chains. Longest chain 18 peptides. Score 0.489 Round 5: 244 peptides, 35 chains. Longest chain 17 peptides. Score 0.493 Taking the results from Round 2 Chains 36, Residues 217, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 7067 reflections ( 99.66 % complete ) and 6516 restraints for refining 3068 atoms. 5654 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2664 (Rfree = 0.000) for 3068 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 37: After refmac, R = 0.2554 (Rfree = 0.000) for 3038 atoms. Found 18 (19 requested) and removed 16 (9 requested) atoms. Cycle 38: After refmac, R = 0.2501 (Rfree = 0.000) for 3034 atoms. Found 12 (19 requested) and removed 13 (9 requested) atoms. Cycle 39: After refmac, R = 0.2402 (Rfree = 0.000) for 3029 atoms. Found 17 (19 requested) and removed 17 (9 requested) atoms. Cycle 40: After refmac, R = 0.2441 (Rfree = 0.000) for 3026 atoms. Found 15 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 2.83 Search for helices and strands: 0 residues in 0 chains, 3154 seeds are put forward Round 1: 209 peptides, 42 chains. Longest chain 10 peptides. Score 0.304 Round 2: 241 peptides, 40 chains. Longest chain 15 peptides. Score 0.425 Round 3: 247 peptides, 39 chains. Longest chain 19 peptides. Score 0.454 Round 4: 247 peptides, 38 chains. Longest chain 16 peptides. Score 0.466 Round 5: 240 peptides, 33 chains. Longest chain 17 peptides. Score 0.506 Taking the results from Round 5 Chains 34, Residues 207, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 7067 reflections ( 99.66 % complete ) and 6724 restraints for refining 3068 atoms. 5895 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2738 (Rfree = 0.000) for 3068 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 42: After refmac, R = 0.2746 (Rfree = 0.000) for 3057 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 43: After refmac, R = 0.2699 (Rfree = 0.000) for 3052 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 44: After refmac, R = 0.2603 (Rfree = 0.000) for 3046 atoms. Found 13 (19 requested) and removed 15 (9 requested) atoms. Cycle 45: After refmac, R = 0.2535 (Rfree = 0.000) for 3042 atoms. Found 16 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.82 Search for helices and strands: 0 residues in 0 chains, 3149 seeds are put forward Round 1: 195 peptides, 35 chains. Longest chain 13 peptides. Score 0.354 Round 2: 197 peptides, 33 chains. Longest chain 13 peptides. Score 0.386 Round 3: 212 peptides, 32 chains. Longest chain 13 peptides. Score 0.442 Round 4: 219 peptides, 32 chains. Longest chain 14 peptides. Score 0.462 Round 5: 220 peptides, 30 chains. Longest chain 20 peptides. Score 0.489 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 190, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 1vra-3_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (190 residues) following loop building 5 chains (35 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7067 reflections ( 99.66 % complete ) and 6481 restraints for refining 3068 atoms. 5653 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2821 (Rfree = 0.000) for 3068 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2711 (Rfree = 0.000) for 3033 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2601 (Rfree = 0.000) for 3016 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2593 (Rfree = 0.000) for 2994 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:27:11 GMT 2018 Job finished. TimeTaking 59.23 Used memory is bytes: 22452416