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 2a3n-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2a3n-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2a3n-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-3.2-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/2a3n-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-3.2-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/2a3n-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2a3n-3.2-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: 0.6284 Checking the provided sequence file Detected sequence length: 355 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 355 Adjusted target solvent content: 0.44 Input MTZ file: 2a3n-3.2-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: 5 Cell parameters: 81.220 102.610 49.296 90.000 123.209 90.000 Input sequence file: 2a3n-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 2840 target number of atoms Had to go as low as 0.75 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: 56.657 3.200 Wilson plot Bfac: 65.62 5624 reflections ( 99.84 % complete ) and 0 restraints for refining 3131 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3202 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2757 (Rfree = 0.000) for 3131 atoms. Found 28 (28 requested) and removed 30 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.22 3.49 Search for helices and strands: 0 residues in 0 chains, 3188 seeds are put forward Round 1: 138 peptides, 28 chains. Longest chain 7 peptides. Score 0.305 Round 2: 171 peptides, 30 chains. Longest chain 18 peptides. Score 0.422 Round 3: 205 peptides, 32 chains. Longest chain 18 peptides. Score 0.527 Round 4: 201 peptides, 29 chains. Longest chain 20 peptides. Score 0.561 Round 5: 218 peptides, 29 chains. Longest chain 20 peptides. Score 0.620 Taking the results from Round 5 Chains 32, Residues 189, Estimated correctness of the model 46.3 % 4 chains (44 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.84 % complete ) and 5143 restraints for refining 2591 atoms. 4244 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2580 (Rfree = 0.000) for 2591 atoms. Found 18 (23 requested) and removed 27 (11 requested) atoms. Cycle 2: After refmac, R = 0.2445 (Rfree = 0.000) for 2554 atoms. Found 11 (23 requested) and removed 13 (11 requested) atoms. Cycle 3: After refmac, R = 0.2429 (Rfree = 0.000) for 2534 atoms. Found 7 (22 requested) and removed 14 (11 requested) atoms. Cycle 4: After refmac, R = 0.2404 (Rfree = 0.000) for 2525 atoms. Found 3 (22 requested) and removed 13 (11 requested) atoms. Cycle 5: After refmac, R = 0.2436 (Rfree = 0.000) for 2505 atoms. Found 10 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 3.44 Search for helices and strands: 0 residues in 0 chains, 2609 seeds are put forward Round 1: 170 peptides, 22 chains. Longest chain 23 peptides. Score 0.562 Round 2: 204 peptides, 28 chains. Longest chain 23 peptides. Score 0.588 Round 3: 199 peptides, 26 chains. Longest chain 23 peptides. Score 0.601 Round 4: 214 peptides, 25 chains. Longest chain 22 peptides. Score 0.664 Round 5: 201 peptides, 28 chains. Longest chain 21 peptides. Score 0.577 Taking the results from Round 4 Chains 27, Residues 189, Estimated correctness of the model 57.2 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.84 % complete ) and 5467 restraints for refining 2591 atoms. 4618 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2534 (Rfree = 0.000) for 2591 atoms. Found 11 (23 requested) and removed 20 (11 requested) atoms. Cycle 7: After refmac, R = 0.2397 (Rfree = 0.000) for 2574 atoms. Found 6 (23 requested) and removed 17 (11 requested) atoms. Cycle 8: After refmac, R = 0.2403 (Rfree = 0.000) for 2554 atoms. Found 8 (22 requested) and removed 13 (11 requested) atoms. Cycle 9: After refmac, R = 0.2262 (Rfree = 0.000) for 2544 atoms. Found 6 (22 requested) and removed 16 (11 requested) atoms. Cycle 10: After refmac, R = 0.2166 (Rfree = 0.000) for 2526 atoms. Found 2 (22 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 2616 seeds are put forward Round 1: 173 peptides, 29 chains. Longest chain 19 peptides. Score 0.450 Round 2: 184 peptides, 23 chains. Longest chain 23 peptides. Score 0.596 Round 3: 201 peptides, 24 chains. Longest chain 21 peptides. Score 0.638 Round 4: 217 peptides, 22 chains. Longest chain 35 peptides. Score 0.711 Round 5: 216 peptides, 23 chains. Longest chain 23 peptides. Score 0.696 Taking the results from Round 4 Chains 22, Residues 195, Estimated correctness of the model 67.5 % 4 chains (74 residues) have been docked in sequence Building loops using Loopy2018 22 chains (195 residues) following loop building 4 chains (74 residues) in sequence following loop building ------------------------------------------------------ 5624 reflections ( 99.84 % complete ) and 4957 restraints for refining 2592 atoms. 3912 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2492 (Rfree = 0.000) for 2592 atoms. Found 16 (23 requested) and removed 27 (11 requested) atoms. Cycle 12: After refmac, R = 0.2559 (Rfree = 0.000) for 2567 atoms. Found 20 (23 requested) and removed 20 (11 requested) atoms. Cycle 13: After refmac, R = 0.2369 (Rfree = 0.000) for 2552 atoms. Found 8 (22 requested) and removed 16 (11 requested) atoms. Cycle 14: After refmac, R = 0.2191 (Rfree = 0.000) for 2536 atoms. Found 8 (21 requested) and removed 12 (11 requested) atoms. Cycle 15: After refmac, R = 0.2459 (Rfree = 0.000) for 2529 atoms. Found 16 (20 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 2624 seeds are put forward Round 1: 183 peptides, 28 chains. Longest chain 15 peptides. Score 0.509 Round 2: 187 peptides, 24 chains. Longest chain 27 peptides. Score 0.591 Round 3: 192 peptides, 23 chains. Longest chain 21 peptides. Score 0.623 Round 4: 175 peptides, 25 chains. Longest chain 22 peptides. Score 0.530 Round 5: 190 peptides, 26 chains. Longest chain 26 peptides. Score 0.570 Taking the results from Round 3 Chains 27, Residues 169, Estimated correctness of the model 47.1 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.84 % complete ) and 5436 restraints for refining 2592 atoms. 4612 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2300 (Rfree = 0.000) for 2592 atoms. Found 15 (21 requested) and removed 18 (11 requested) atoms. Cycle 17: After refmac, R = 0.2119 (Rfree = 0.000) for 2582 atoms. Found 5 (21 requested) and removed 13 (11 requested) atoms. Cycle 18: After refmac, R = 0.2124 (Rfree = 0.000) for 2570 atoms. Found 2 (21 requested) and removed 13 (11 requested) atoms. Cycle 19: After refmac, R = 0.2021 (Rfree = 0.000) for 2556 atoms. Found 5 (20 requested) and removed 14 (11 requested) atoms. Cycle 20: After refmac, R = 0.1935 (Rfree = 0.000) for 2543 atoms. Found 6 (20 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.14 3.40 Search for helices and strands: 0 residues in 0 chains, 2638 seeds are put forward Round 1: 174 peptides, 28 chains. Longest chain 16 peptides. Score 0.472 Round 2: 191 peptides, 28 chains. Longest chain 21 peptides. Score 0.540 Round 3: 189 peptides, 26 chains. Longest chain 21 peptides. Score 0.566 Round 4: 195 peptides, 28 chains. Longest chain 21 peptides. Score 0.555 Round 5: 182 peptides, 27 chains. Longest chain 16 peptides. Score 0.522 Taking the results from Round 3 Chains 28, Residues 163, Estimated correctness of the model 31.6 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.84 % complete ) and 5654 restraints for refining 2592 atoms. 4950 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2238 (Rfree = 0.000) for 2592 atoms. Found 16 (21 requested) and removed 16 (11 requested) atoms. Cycle 22: After refmac, R = 0.2081 (Rfree = 0.000) for 2583 atoms. Found 13 (21 requested) and removed 17 (11 requested) atoms. Cycle 23: After refmac, R = 0.2176 (Rfree = 0.000) for 2571 atoms. Found 15 (21 requested) and removed 13 (11 requested) atoms. Cycle 24: After refmac, R = 0.1821 (Rfree = 0.000) for 2569 atoms. Found 6 (21 requested) and removed 18 (11 requested) atoms. Cycle 25: After refmac, R = 0.1756 (Rfree = 0.000) for 2552 atoms. Found 6 (20 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 3.42 Search for helices and strands: 0 residues in 0 chains, 2649 seeds are put forward Round 1: 148 peptides, 25 chains. Longest chain 16 peptides. Score 0.415 Round 2: 172 peptides, 27 chains. Longest chain 17 peptides. Score 0.482 Round 3: 186 peptides, 30 chains. Longest chain 17 peptides. Score 0.486 Round 4: 169 peptides, 27 chains. Longest chain 17 peptides. Score 0.469 Round 5: 174 peptides, 25 chains. Longest chain 17 peptides. Score 0.526 Taking the results from Round 5 Chains 25, Residues 149, Estimated correctness of the model 19.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.84 % complete ) and 5733 restraints for refining 2575 atoms. 5126 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2069 (Rfree = 0.000) for 2575 atoms. Found 19 (21 requested) and removed 16 (11 requested) atoms. Cycle 27: After refmac, R = 0.2307 (Rfree = 0.000) for 2576 atoms. Found 21 (21 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.1856 (Rfree = 0.000) for 2580 atoms. Found 9 (21 requested) and removed 14 (11 requested) atoms. Cycle 29: After refmac, R = 0.1782 (Rfree = 0.000) for 2570 atoms. Found 11 (21 requested) and removed 13 (11 requested) atoms. Cycle 30: After refmac, R = 0.1793 (Rfree = 0.000) for 2566 atoms. Found 15 (21 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 2676 seeds are put forward Round 1: 146 peptides, 24 chains. Longest chain 14 peptides. Score 0.426 Round 2: 161 peptides, 25 chains. Longest chain 14 peptides. Score 0.472 Round 3: 160 peptides, 22 chains. Longest chain 19 peptides. Score 0.523 Round 4: 166 peptides, 22 chains. Longest chain 21 peptides. Score 0.546 Round 5: 164 peptides, 25 chains. Longest chain 13 peptides. Score 0.485 Taking the results from Round 4 Chains 23, Residues 144, Estimated correctness of the model 25.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.84 % complete ) and 5710 restraints for refining 2575 atoms. 5134 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2081 (Rfree = 0.000) for 2575 atoms. Found 18 (21 requested) and removed 22 (11 requested) atoms. Cycle 32: After refmac, R = 0.1918 (Rfree = 0.000) for 2566 atoms. Found 14 (21 requested) and removed 15 (11 requested) atoms. Cycle 33: After refmac, R = 0.1644 (Rfree = 0.000) for 2558 atoms. Found 6 (21 requested) and removed 12 (11 requested) atoms. Cycle 34: After refmac, R = 0.1609 (Rfree = 0.000) for 2547 atoms. Found 14 (20 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.1511 (Rfree = 0.000) for 2544 atoms. Found 3 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.13 3.39 Search for helices and strands: 0 residues in 0 chains, 2635 seeds are put forward Round 1: 132 peptides, 23 chains. Longest chain 13 peptides. Score 0.380 Round 2: 141 peptides, 24 chains. Longest chain 17 peptides. Score 0.403 Round 3: 162 peptides, 24 chains. Longest chain 18 peptides. Score 0.495 Round 4: 156 peptides, 23 chains. Longest chain 16 peptides. Score 0.488 Round 5: 146 peptides, 22 chains. Longest chain 18 peptides. Score 0.464 Taking the results from Round 3 Chains 24, Residues 138, Estimated correctness of the model 9.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.84 % complete ) and 5819 restraints for refining 2579 atoms. 5291 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1847 (Rfree = 0.000) for 2579 atoms. Found 16 (21 requested) and removed 21 (11 requested) atoms. Cycle 37: After refmac, R = 0.1773 (Rfree = 0.000) for 2571 atoms. Found 15 (21 requested) and removed 12 (11 requested) atoms. Cycle 38: After refmac, R = 0.1749 (Rfree = 0.000) for 2570 atoms. Found 14 (21 requested) and removed 13 (11 requested) atoms. Cycle 39: After refmac, R = 0.1597 (Rfree = 0.000) for 2567 atoms. Found 7 (21 requested) and removed 27 (11 requested) atoms. Cycle 40: After refmac, R = 0.1472 (Rfree = 0.000) for 2543 atoms. Found 11 (20 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.15 3.41 Search for helices and strands: 0 residues in 0 chains, 2643 seeds are put forward Round 1: 130 peptides, 24 chains. Longest chain 14 peptides. Score 0.350 Round 2: 158 peptides, 22 chains. Longest chain 19 peptides. Score 0.515 Round 3: 164 peptides, 22 chains. Longest chain 21 peptides. Score 0.539 Round 4: 148 peptides, 23 chains. Longest chain 13 peptides. Score 0.454 Round 5: 159 peptides, 26 chains. Longest chain 11 peptides. Score 0.445 Taking the results from Round 3 Chains 22, Residues 142, Estimated correctness of the model 23.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5624 reflections ( 99.84 % complete ) and 5673 restraints for refining 2567 atoms. 5127 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1668 (Rfree = 0.000) for 2567 atoms. Found 15 (21 requested) and removed 13 (11 requested) atoms. Cycle 42: After refmac, R = 0.1436 (Rfree = 0.000) for 2566 atoms. Found 3 (21 requested) and removed 11 (11 requested) atoms. Cycle 43: After refmac, R = 0.1412 (Rfree = 0.000) for 2558 atoms. Found 1 (20 requested) and removed 11 (11 requested) atoms. Cycle 44: After refmac, R = 0.1340 (Rfree = 0.000) for 2545 atoms. Found 8 (20 requested) and removed 12 (11 requested) atoms. Cycle 45: After refmac, R = 0.1307 (Rfree = 0.000) for 2540 atoms. Found 6 (20 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.20 3.47 Search for helices and strands: 0 residues in 0 chains, 2629 seeds are put forward Round 1: 128 peptides, 20 chains. Longest chain 17 peptides. Score 0.423 Round 2: 136 peptides, 20 chains. Longest chain 19 peptides. Score 0.460 Round 3: 143 peptides, 19 chains. Longest chain 20 peptides. Score 0.509 Round 4: 147 peptides, 20 chains. Longest chain 20 peptides. Score 0.507 Round 5: 146 peptides, 20 chains. Longest chain 20 peptides. Score 0.502 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 124, Estimated correctness of the model 14.2 % 2 chains (22 residues) have been docked in sequence Sequence coverage is 17 % Consider running further cycles of model building using 2a3n-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (124 residues) following loop building 2 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5624 reflections ( 99.84 % complete ) and 5616 restraints for refining 2569 atoms. 5061 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1494 (Rfree = 0.000) for 2569 atoms. Found 0 (21 requested) and removed 10 (11 requested) atoms. Cycle 47: After refmac, R = 0.1488 (Rfree = 0.000) for 2552 atoms. Found 0 (20 requested) and removed 3 (11 requested) atoms. Cycle 48: After refmac, R = 0.1495 (Rfree = 0.000) for 2549 atoms. Found 0 (20 requested) and removed 4 (11 requested) atoms. Cycle 49: After refmac, R = 0.1516 (Rfree = 0.000) for 2541 atoms. Found 0 (20 requested) and removed 7 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:14:42 GMT 2018 Job finished. TimeTaking 46.79 Used memory is bytes: 10248880