null Sun 23 Dec 22:23:05 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 1zyb-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-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/1zyb-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-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 ============================================================ Sun 23 Dec 22:23:14 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/1zyb-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-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 286 and 0 Target number of residues in the AU: 286 Target solvent content: 0.6668 Checking the provided sequence file Detected sequence length: 232 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 232 Adjusted target solvent content: 0.73 Input MTZ file: 1zyb-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: 179 Cell parameters: 115.980 115.980 119.640 90.000 90.000 120.000 Input sequence file: 1zyb-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1856 target number of atoms Had to go as low as 1.30 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: 100.441 4.000 Wilson plot Bfac: 89.66 4315 reflections ( 99.10 % complete ) and 0 restraints for refining 2049 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3848 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2990 (Rfree = 0.000) for 2049 atoms. Found 9 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.79 2.72 Search for helices and strands: 0 residues in 0 chains, 2079 seeds are put forward Round 1: 161 peptides, 21 chains. Longest chain 15 peptides. Score 0.474 Round 2: 168 peptides, 15 chains. Longest chain 28 peptides. Score 0.582 Round 3: 174 peptides, 16 chains. Longest chain 31 peptides. Score 0.585 Round 4: 172 peptides, 13 chains. Longest chain 41 peptides. Score 0.619 Round 5: 160 peptides, 13 chains. Longest chain 39 peptides. Score 0.587 Taking the results from Round 4 Chains 13, Residues 159, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4315 reflections ( 99.10 % complete ) and 3617 restraints for refining 1675 atoms. 2994 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3090 (Rfree = 0.000) for 1675 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 2: After refmac, R = 0.2953 (Rfree = 0.000) for 1653 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 3: After refmac, R = 0.2828 (Rfree = 0.000) for 1632 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 4: After refmac, R = 0.2713 (Rfree = 0.000) for 1623 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2660 (Rfree = 0.000) for 1612 atoms. Found 5 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 2.74 Search for helices and strands: 0 residues in 0 chains, 1694 seeds are put forward Round 1: 162 peptides, 18 chains. Longest chain 27 peptides. Score 0.522 Round 2: 156 peptides, 15 chains. Longest chain 36 peptides. Score 0.547 Round 3: 165 peptides, 15 chains. Longest chain 32 peptides. Score 0.573 Round 4: 153 peptides, 15 chains. Longest chain 18 peptides. Score 0.538 Round 5: 164 peptides, 18 chains. Longest chain 21 peptides. Score 0.528 Taking the results from Round 3 Chains 15, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4315 reflections ( 99.10 % complete ) and 3532 restraints for refining 1676 atoms. 2947 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2937 (Rfree = 0.000) for 1676 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 7: After refmac, R = 0.2790 (Rfree = 0.000) for 1659 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 8: After refmac, R = 0.2738 (Rfree = 0.000) for 1652 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 9: After refmac, R = 0.2695 (Rfree = 0.000) for 1649 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2682 (Rfree = 0.000) for 1648 atoms. Found 6 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.82 2.74 Search for helices and strands: 0 residues in 0 chains, 1725 seeds are put forward Round 1: 165 peptides, 20 chains. Longest chain 18 peptides. Score 0.502 Round 2: 168 peptides, 17 chains. Longest chain 19 peptides. Score 0.554 Round 3: 163 peptides, 15 chains. Longest chain 23 peptides. Score 0.568 Round 4: 160 peptides, 16 chains. Longest chain 18 peptides. Score 0.545 Round 5: 159 peptides, 16 chains. Longest chain 35 peptides. Score 0.542 Taking the results from Round 3 Chains 15, Residues 148, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4315 reflections ( 99.10 % complete ) and 3648 restraints for refining 1676 atoms. 3071 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2828 (Rfree = 0.000) for 1676 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 12: After refmac, R = 0.2606 (Rfree = 0.000) for 1657 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.2457 (Rfree = 0.000) for 1650 atoms. Found 2 (7 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.2388 (Rfree = 0.000) for 1632 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.2341 (Rfree = 0.000) for 1625 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.78 2.71 Search for helices and strands: 0 residues in 0 chains, 1691 seeds are put forward Round 1: 155 peptides, 18 chains. Longest chain 22 peptides. Score 0.500 Round 2: 162 peptides, 18 chains. Longest chain 18 peptides. Score 0.522 Round 3: 163 peptides, 16 chains. Longest chain 23 peptides. Score 0.554 Round 4: 159 peptides, 17 chains. Longest chain 19 peptides. Score 0.527 Round 5: 163 peptides, 14 chains. Longest chain 22 peptides. Score 0.582 Taking the results from Round 5 Chains 14, Residues 149, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4315 reflections ( 99.10 % complete ) and 3622 restraints for refining 1676 atoms. 3040 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2498 (Rfree = 0.000) for 1676 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 17: After refmac, R = 0.2268 (Rfree = 0.000) for 1663 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2193 (Rfree = 0.000) for 1657 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2130 (Rfree = 0.000) for 1652 atoms. Found 3 (7 requested) and removed 6 (3 requested) atoms. Cycle 20: After refmac, R = 0.2075 (Rfree = 0.000) for 1645 atoms. Found 0 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.75 2.69 Search for helices and strands: 0 residues in 0 chains, 1722 seeds are put forward Round 1: 155 peptides, 22 chains. Longest chain 14 peptides. Score 0.439 Round 2: 156 peptides, 15 chains. Longest chain 26 peptides. Score 0.547 Round 3: 151 peptides, 16 chains. Longest chain 20 peptides. Score 0.518 Round 4: 153 peptides, 18 chains. Longest chain 17 peptides. Score 0.494 Round 5: 158 peptides, 15 chains. Longest chain 24 peptides. Score 0.553 Taking the results from Round 5 Chains 15, Residues 143, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4315 reflections ( 99.10 % complete ) and 3523 restraints for refining 1676 atoms. 2966 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2644 (Rfree = 0.000) for 1676 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 22: After refmac, R = 0.2497 (Rfree = 0.000) for 1649 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 23: After refmac, R = 0.2423 (Rfree = 0.000) for 1628 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 24: After refmac, R = 0.2338 (Rfree = 0.000) for 1617 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 25: After refmac, R = 0.2211 (Rfree = 0.000) for 1612 atoms. Found 5 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.75 2.69 Search for helices and strands: 0 residues in 0 chains, 1730 seeds are put forward Round 1: 139 peptides, 20 chains. Longest chain 14 peptides. Score 0.415 Round 2: 160 peptides, 19 chains. Longest chain 33 peptides. Score 0.501 Round 3: 165 peptides, 19 chains. Longest chain 36 peptides. Score 0.517 Round 4: 154 peptides, 16 chains. Longest chain 31 peptides. Score 0.527 Round 5: 165 peptides, 15 chains. Longest chain 48 peptides. Score 0.573 Taking the results from Round 5 Chains 15, Residues 150, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4315 reflections ( 99.10 % complete ) and 3537 restraints for refining 1675 atoms. 2952 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2782 (Rfree = 0.000) for 1675 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 27: After refmac, R = 0.2514 (Rfree = 0.000) for 1645 atoms. Found 5 (7 requested) and removed 5 (3 requested) atoms. Cycle 28: After refmac, R = 0.2378 (Rfree = 0.000) for 1637 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.2451 (Rfree = 0.000) for 1626 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 30: After refmac, R = 0.2467 (Rfree = 0.000) for 1621 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 2.74 Search for helices and strands: 0 residues in 0 chains, 1725 seeds are put forward Round 1: 140 peptides, 19 chains. Longest chain 14 peptides. Score 0.435 Round 2: 151 peptides, 15 chains. Longest chain 23 peptides. Score 0.532 Round 3: 159 peptides, 18 chains. Longest chain 17 peptides. Score 0.513 Round 4: 160 peptides, 18 chains. Longest chain 28 peptides. Score 0.516 Round 5: 159 peptides, 17 chains. Longest chain 19 peptides. Score 0.527 Taking the results from Round 2 Chains 15, Residues 136, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4315 reflections ( 99.10 % complete ) and 3575 restraints for refining 1676 atoms. 3046 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2410 (Rfree = 0.000) for 1676 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 32: After refmac, R = 0.2270 (Rfree = 0.000) for 1655 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 33: After refmac, R = 0.2509 (Rfree = 0.000) for 1637 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 34: After refmac, R = 0.2221 (Rfree = 0.000) for 1616 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.2177 (Rfree = 0.000) for 1609 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.74 2.69 Search for helices and strands: 0 residues in 0 chains, 1692 seeds are put forward Round 1: 148 peptides, 23 chains. Longest chain 13 peptides. Score 0.399 Round 2: 162 peptides, 16 chains. Longest chain 26 peptides. Score 0.551 Round 3: 158 peptides, 19 chains. Longest chain 18 peptides. Score 0.495 Round 4: 160 peptides, 13 chains. Longest chain 26 peptides. Score 0.587 Round 5: 155 peptides, 18 chains. Longest chain 23 peptides. Score 0.500 Taking the results from Round 4 Chains 15, Residues 147, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4315 reflections ( 99.10 % complete ) and 3436 restraints for refining 1676 atoms. 2826 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2594 (Rfree = 0.000) for 1676 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 37: After refmac, R = 0.2357 (Rfree = 0.000) for 1661 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.2233 (Rfree = 0.000) for 1656 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 39: After refmac, R = 0.2160 (Rfree = 0.000) for 1651 atoms. Found 2 (7 requested) and removed 7 (3 requested) atoms. Cycle 40: After refmac, R = 0.2088 (Rfree = 0.000) for 1646 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 2.71 Search for helices and strands: 0 residues in 0 chains, 1727 seeds are put forward Round 1: 150 peptides, 20 chains. Longest chain 15 peptides. Score 0.453 Round 2: 158 peptides, 16 chains. Longest chain 27 peptides. Score 0.539 Round 3: 154 peptides, 14 chains. Longest chain 25 peptides. Score 0.556 Round 4: 167 peptides, 17 chains. Longest chain 23 peptides. Score 0.551 Round 5: 157 peptides, 12 chains. Longest chain 35 peptides. Score 0.593 Taking the results from Round 5 Chains 12, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4315 reflections ( 99.10 % complete ) and 3532 restraints for refining 1675 atoms. 2964 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2609 (Rfree = 0.000) for 1675 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 42: After refmac, R = 0.2319 (Rfree = 0.000) for 1662 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2246 (Rfree = 0.000) for 1657 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. Cycle 44: After refmac, R = 0.2140 (Rfree = 0.000) for 1649 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.2009 (Rfree = 0.000) for 1645 atoms. Found 3 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 2.71 Search for helices and strands: 0 residues in 0 chains, 1710 seeds are put forward Round 1: 151 peptides, 18 chains. Longest chain 22 peptides. Score 0.487 Round 2: 163 peptides, 19 chains. Longest chain 22 peptides. Score 0.510 Round 3: 170 peptides, 17 chains. Longest chain 23 peptides. Score 0.560 Round 4: 163 peptides, 20 chains. Longest chain 18 peptides. Score 0.496 Round 5: 160 peptides, 18 chains. Longest chain 25 peptides. Score 0.516 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 153, 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 1zyb-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4315 reflections ( 99.10 % complete ) and 3572 restraints for refining 1676 atoms. 2977 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2520 (Rfree = 0.000) for 1676 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2301 (Rfree = 0.000) for 1664 atoms. Found 0 (7 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2269 (Rfree = 0.000) for 1655 atoms. Found 0 (7 requested) and removed 2 (3 requested) atoms. Cycle 49: After refmac, R = 0.2235 (Rfree = 0.000) for 1653 atoms. Found 0 (7 requested) and removed 0 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:08:50 GMT 2018 Job finished. TimeTaking 45.77 Used memory is bytes: 4938264