Tue 25 Dec 19:27:56 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-3.8-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 19:28:10 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-3.8-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 293 and 0 Target number of residues in the AU: 293 Target solvent content: 0.6587 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 83.87 5018 reflections ( 99.23 % complete ) and 0 restraints for refining 2052 atoms. Observations/parameters ratio is 0.61 ------------------------------------------------------ Starting model: R = 0.3904 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3727 (Rfree = 0.000) for 2052 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 2.71 Search for helices and strands: 0 residues in 0 chains, 2109 seeds are put forward Round 1: 129 peptides, 22 chains. Longest chain 12 peptides. Score 0.345 Round 2: 152 peptides, 16 chains. Longest chain 37 peptides. Score 0.521 Round 3: 151 peptides, 15 chains. Longest chain 32 peptides. Score 0.532 Round 4: 148 peptides, 14 chains. Longest chain 30 peptides. Score 0.538 Round 5: 151 peptides, 17 chains. Longest chain 20 peptides. Score 0.503 Taking the results from Round 4 Chains 14, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5018 reflections ( 99.23 % complete ) and 3709 restraints for refining 1678 atoms. 3187 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3450 (Rfree = 0.000) for 1678 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 2: After refmac, R = 0.3543 (Rfree = 0.000) for 1634 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 3: After refmac, R = 0.3064 (Rfree = 0.000) for 1592 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 4: After refmac, R = 0.2982 (Rfree = 0.000) for 1569 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 5: After refmac, R = 0.3015 (Rfree = 0.000) for 1554 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 2.64 Search for helices and strands: 0 residues in 0 chains, 1640 seeds are put forward Round 1: 164 peptides, 18 chains. Longest chain 25 peptides. Score 0.528 Round 2: 170 peptides, 15 chains. Longest chain 30 peptides. Score 0.587 Round 3: 174 peptides, 16 chains. Longest chain 26 peptides. Score 0.585 Round 4: 171 peptides, 16 chains. Longest chain 27 peptides. Score 0.577 Round 5: 169 peptides, 16 chains. Longest chain 22 peptides. Score 0.571 Taking the results from Round 2 Chains 17, Residues 155, Estimated correctness of the model 0.0 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 5018 reflections ( 99.23 % complete ) and 3119 restraints for refining 1679 atoms. 2374 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3107 (Rfree = 0.000) for 1679 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2861 (Rfree = 0.000) for 1651 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 8: After refmac, R = 0.2792 (Rfree = 0.000) for 1629 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 9: After refmac, R = 0.2783 (Rfree = 0.000) for 1610 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2989 (Rfree = 0.000) for 1598 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 2.66 Search for helices and strands: 0 residues in 0 chains, 1685 seeds are put forward Round 1: 167 peptides, 18 chains. Longest chain 29 peptides. Score 0.537 Round 2: 178 peptides, 15 chains. Longest chain 35 peptides. Score 0.609 Round 3: 173 peptides, 16 chains. Longest chain 26 peptides. Score 0.582 Round 4: 166 peptides, 16 chains. Longest chain 32 peptides. Score 0.562 Round 5: 179 peptides, 18 chains. Longest chain 19 peptides. Score 0.572 Taking the results from Round 2 Chains 17, Residues 163, Estimated correctness of the model 3.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5018 reflections ( 99.23 % complete ) and 3125 restraints for refining 1679 atoms. 2384 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3246 (Rfree = 0.000) for 1679 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 12: After refmac, R = 0.3200 (Rfree = 0.000) for 1648 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 13: After refmac, R = 0.3214 (Rfree = 0.000) for 1612 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.3142 (Rfree = 0.000) for 1586 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 15: After refmac, R = 0.2901 (Rfree = 0.000) for 1569 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.68 2.64 Search for helices and strands: 0 residues in 0 chains, 1676 seeds are put forward Round 1: 162 peptides, 19 chains. Longest chain 21 peptides. Score 0.507 Round 2: 173 peptides, 13 chains. Longest chain 24 peptides. Score 0.622 Round 3: 163 peptides, 15 chains. Longest chain 26 peptides. Score 0.568 Round 4: 166 peptides, 17 chains. Longest chain 22 peptides. Score 0.548 Round 5: 175 peptides, 16 chains. Longest chain 23 peptides. Score 0.588 Taking the results from Round 2 Chains 13, Residues 160, Estimated correctness of the model 8.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5018 reflections ( 99.23 % complete ) and 3384 restraints for refining 1650 atoms. 2757 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3046 (Rfree = 0.000) for 1650 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 17: After refmac, R = 0.2719 (Rfree = 0.000) for 1628 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2671 (Rfree = 0.000) for 1614 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2588 (Rfree = 0.000) for 1595 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.2336 (Rfree = 0.000) for 1586 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.63 2.61 Search for helices and strands: 0 residues in 0 chains, 1678 seeds are put forward Round 1: 167 peptides, 21 chains. Longest chain 16 peptides. Score 0.494 Round 2: 170 peptides, 15 chains. Longest chain 36 peptides. Score 0.587 Round 3: 172 peptides, 17 chains. Longest chain 28 peptides. Score 0.566 Round 4: 167 peptides, 13 chains. Longest chain 29 peptides. Score 0.606 Round 5: 169 peptides, 16 chains. Longest chain 24 peptides. Score 0.571 Taking the results from Round 4 Chains 13, Residues 154, Estimated correctness of the model 1.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5018 reflections ( 99.23 % complete ) and 3496 restraints for refining 1679 atoms. 2893 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3093 (Rfree = 0.000) for 1679 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2697 (Rfree = 0.000) for 1656 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 23: After refmac, R = 0.2706 (Rfree = 0.000) for 1644 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 24: After refmac, R = 0.2492 (Rfree = 0.000) for 1631 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2477 (Rfree = 0.000) for 1626 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 2.58 Search for helices and strands: 0 residues in 0 chains, 1719 seeds are put forward Round 1: 158 peptides, 19 chains. Longest chain 19 peptides. Score 0.495 Round 2: 181 peptides, 18 chains. Longest chain 31 peptides. Score 0.578 Round 3: 180 peptides, 12 chains. Longest chain 37 peptides. Score 0.652 Round 4: 178 peptides, 16 chains. Longest chain 27 peptides. Score 0.596 Round 5: 170 peptides, 14 chains. Longest chain 27 peptides. Score 0.601 Taking the results from Round 3 Chains 13, Residues 168, Estimated correctness of the model 21.6 % 1 chains (34 residues) have been docked in sequence ------------------------------------------------------ 5018 reflections ( 99.23 % complete ) and 2951 restraints for refining 1679 atoms. 2133 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3121 (Rfree = 0.000) for 1679 atoms. Found 9 (9 requested) and removed 23 (4 requested) atoms. Cycle 27: After refmac, R = 0.2546 (Rfree = 0.000) for 1642 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 28: After refmac, R = 0.2376 (Rfree = 0.000) for 1633 atoms. Found 8 (9 requested) and removed 7 (4 requested) atoms. Cycle 29: After refmac, R = 0.2523 (Rfree = 0.000) for 1627 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 30: After refmac, R = 0.2251 (Rfree = 0.000) for 1612 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 2.59 Search for helices and strands: 0 residues in 0 chains, 1675 seeds are put forward Round 1: 160 peptides, 16 chains. Longest chain 23 peptides. Score 0.545 Round 2: 177 peptides, 15 chains. Longest chain 27 peptides. Score 0.606 Round 3: 180 peptides, 15 chains. Longest chain 29 peptides. Score 0.614 Round 4: 186 peptides, 14 chains. Longest chain 33 peptides. Score 0.642 Round 5: 166 peptides, 15 chains. Longest chain 24 peptides. Score 0.576 Taking the results from Round 4 Chains 15, Residues 172, Estimated correctness of the model 17.5 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5018 reflections ( 99.23 % complete ) and 3212 restraints for refining 1679 atoms. 2467 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2909 (Rfree = 0.000) for 1679 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 32: After refmac, R = 0.2630 (Rfree = 0.000) for 1663 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2685 (Rfree = 0.000) for 1648 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2173 (Rfree = 0.000) for 1635 atoms. Found 8 (9 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.2132 (Rfree = 0.000) for 1637 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 2.58 Search for helices and strands: 0 residues in 0 chains, 1727 seeds are put forward Round 1: 171 peptides, 19 chains. Longest chain 24 peptides. Score 0.535 Round 2: 173 peptides, 14 chains. Longest chain 29 peptides. Score 0.609 Round 3: 180 peptides, 16 chains. Longest chain 29 peptides. Score 0.601 Round 4: 170 peptides, 14 chains. Longest chain 24 peptides. Score 0.601 Round 5: 175 peptides, 14 chains. Longest chain 26 peptides. Score 0.614 Taking the results from Round 5 Chains 15, Residues 161, Estimated correctness of the model 5.3 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5018 reflections ( 99.23 % complete ) and 3271 restraints for refining 1679 atoms. 2546 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3065 (Rfree = 0.000) for 1679 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2767 (Rfree = 0.000) for 1666 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 38: After refmac, R = 0.2631 (Rfree = 0.000) for 1656 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2539 (Rfree = 0.000) for 1652 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2505 (Rfree = 0.000) for 1647 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.66 2.63 Search for helices and strands: 0 residues in 0 chains, 1708 seeds are put forward Round 1: 155 peptides, 20 chains. Longest chain 15 peptides. Score 0.470 Round 2: 169 peptides, 18 chains. Longest chain 27 peptides. Score 0.543 Round 3: 172 peptides, 19 chains. Longest chain 19 peptides. Score 0.538 Round 4: 177 peptides, 15 chains. Longest chain 48 peptides. Score 0.606 Round 5: 169 peptides, 17 chains. Longest chain 20 peptides. Score 0.557 Taking the results from Round 4 Chains 15, Residues 162, Estimated correctness of the model 1.7 % 1 chains (47 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5018 reflections ( 99.23 % complete ) and 3013 restraints for refining 1678 atoms. 2177 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3161 (Rfree = 0.000) for 1678 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2701 (Rfree = 0.000) for 1649 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 43: After refmac, R = 0.2497 (Rfree = 0.000) for 1634 atoms. Found 8 (9 requested) and removed 9 (4 requested) atoms. Cycle 44: After refmac, R = 0.2390 (Rfree = 0.000) for 1632 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.2309 (Rfree = 0.000) for 1630 atoms. Found 4 (8 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 2.64 Search for helices and strands: 0 residues in 0 chains, 1677 seeds are put forward Round 1: 170 peptides, 21 chains. Longest chain 17 peptides. Score 0.503 Round 2: 175 peptides, 17 chains. Longest chain 23 peptides. Score 0.574 Round 3: 165 peptides, 19 chains. Longest chain 25 peptides. Score 0.517 Round 4: 166 peptides, 15 chains. Longest chain 29 peptides. Score 0.576 Round 5: 168 peptides, 16 chains. Longest chain 21 peptides. Score 0.568 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 151, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5018 reflections ( 99.23 % complete ) and 3592 restraints for refining 1679 atoms. 3003 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3056 (Rfree = 0.000) for 1679 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2603 (Rfree = 0.000) for 1659 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2502 (Rfree = 0.000) for 1651 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2432 (Rfree = 0.000) for 1642 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 20:25:57 GMT 2018 Job finished. TimeTaking 58.02