Sun 23 Dec 22:22:59 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 2gm6-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gm6-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.4-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/2gm6-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.4-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 ============================================================ Sun 23 Dec 22:23:08 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/2gm6-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gm6-3.4-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 232 and 0 Target number of residues in the AU: 232 Target solvent content: 0.6433 Checking the provided sequence file Detected sequence length: 208 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 208 Adjusted target solvent content: 0.68 Input MTZ file: 2gm6-3.4-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: 92 Cell parameters: 57.001 57.001 216.648 90.000 90.000 90.000 Input sequence file: 2gm6-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1664 target number of atoms Had to go as low as 1.00 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: 55.125 3.400 Wilson plot Bfac: 73.48 5424 reflections ( 99.76 % complete ) and 0 restraints for refining 1862 atoms. Observations/parameters ratio is 0.73 ------------------------------------------------------ Starting model: R = 0.3506 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3485 (Rfree = 0.000) for 1862 atoms. Found 14 (14 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.44 2.68 Search for helices and strands: 0 residues in 0 chains, 1908 seeds are put forward Round 1: 117 peptides, 18 chains. Longest chain 12 peptides. Score 0.410 Round 2: 147 peptides, 12 chains. Longest chain 34 peptides. Score 0.640 Round 3: 143 peptides, 16 chains. Longest chain 22 peptides. Score 0.558 Round 4: 159 peptides, 15 chains. Longest chain 28 peptides. Score 0.631 Round 5: 151 peptides, 14 chains. Longest chain 30 peptides. Score 0.620 Taking the results from Round 2 Chains 15, Residues 135, Estimated correctness of the model 41.2 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 5424 reflections ( 99.76 % complete ) and 3013 restraints for refining 1566 atoms. 2358 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3511 (Rfree = 0.000) for 1566 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 2: After refmac, R = 0.3036 (Rfree = 0.000) for 1535 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.3017 (Rfree = 0.000) for 1525 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 4: After refmac, R = 0.2980 (Rfree = 0.000) for 1516 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 5: After refmac, R = 0.2777 (Rfree = 0.000) for 1517 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 2.65 Search for helices and strands: 0 residues in 0 chains, 1586 seeds are put forward Round 1: 138 peptides, 15 chains. Longest chain 19 peptides. Score 0.557 Round 2: 154 peptides, 13 chains. Longest chain 25 peptides. Score 0.646 Round 3: 150 peptides, 13 chains. Longest chain 29 peptides. Score 0.633 Round 4: 141 peptides, 13 chains. Longest chain 22 peptides. Score 0.603 Round 5: 149 peptides, 12 chains. Longest chain 29 peptides. Score 0.646 Taking the results from Round 5 Chains 14, Residues 137, Estimated correctness of the model 43.0 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 5424 reflections ( 99.76 % complete ) and 2798 restraints for refining 1513 atoms. 2088 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3247 (Rfree = 0.000) for 1513 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 7: After refmac, R = 0.2997 (Rfree = 0.000) for 1489 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 8: After refmac, R = 0.2783 (Rfree = 0.000) for 1488 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. Cycle 9: After refmac, R = 0.2497 (Rfree = 0.000) for 1486 atoms. Found 11 (11 requested) and removed 5 (5 requested) atoms. Cycle 10: After refmac, R = 0.2385 (Rfree = 0.000) for 1486 atoms. Found 9 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 2.81 Search for helices and strands: 0 residues in 0 chains, 1533 seeds are put forward Round 1: 154 peptides, 15 chains. Longest chain 27 peptides. Score 0.614 Round 2: 166 peptides, 16 chains. Longest chain 26 peptides. Score 0.638 Round 3: 169 peptides, 14 chains. Longest chain 48 peptides. Score 0.677 Round 4: 169 peptides, 12 chains. Longest chain 55 peptides. Score 0.705 Round 5: 170 peptides, 11 chains. Longest chain 36 peptides. Score 0.722 Taking the results from Round 5 Chains 15, Residues 159, Estimated correctness of the model 63.4 % 4 chains (80 residues) have been docked in sequence Building loops using Loopy2018 15 chains (159 residues) following loop building 4 chains (80 residues) in sequence following loop building ------------------------------------------------------ 5424 reflections ( 99.76 % complete ) and 2455 restraints for refining 1529 atoms. 1496 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2984 (Rfree = 0.000) for 1529 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 12: After refmac, R = 0.2992 (Rfree = 0.000) for 1517 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 13: After refmac, R = 0.2927 (Rfree = 0.000) for 1504 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 14: After refmac, R = 0.2732 (Rfree = 0.000) for 1502 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 15: After refmac, R = 0.2569 (Rfree = 0.000) for 1496 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 2.61 Search for helices and strands: 0 residues in 0 chains, 1537 seeds are put forward Round 1: 162 peptides, 14 chains. Longest chain 27 peptides. Score 0.656 Round 2: 162 peptides, 13 chains. Longest chain 36 peptides. Score 0.671 Round 3: 164 peptides, 13 chains. Longest chain 61 peptides. Score 0.677 Round 4: 163 peptides, 12 chains. Longest chain 40 peptides. Score 0.689 Round 5: 158 peptides, 12 chains. Longest chain 38 peptides. Score 0.674 Taking the results from Round 4 Chains 14, Residues 151, Estimated correctness of the model 55.0 % 3 chains (61 residues) have been docked in sequence ------------------------------------------------------ 5424 reflections ( 99.76 % complete ) and 2566 restraints for refining 1513 atoms. 1709 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2843 (Rfree = 0.000) for 1513 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 17: After refmac, R = 0.2790 (Rfree = 0.000) for 1494 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 18: After refmac, R = 0.2942 (Rfree = 0.000) for 1482 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 19: After refmac, R = 0.2920 (Rfree = 0.000) for 1472 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 20: After refmac, R = 0.2405 (Rfree = 0.000) for 1467 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 1513 seeds are put forward Round 1: 148 peptides, 16 chains. Longest chain 23 peptides. Score 0.577 Round 2: 157 peptides, 15 chains. Longest chain 25 peptides. Score 0.624 Round 3: 163 peptides, 14 chains. Longest chain 28 peptides. Score 0.659 Round 4: 140 peptides, 13 chains. Longest chain 32 peptides. Score 0.599 Round 5: 154 peptides, 10 chains. Longest chain 44 peptides. Score 0.692 Taking the results from Round 5 Chains 12, Residues 144, Estimated correctness of the model 55.8 % 3 chains (83 residues) have been docked in sequence ------------------------------------------------------ 5424 reflections ( 99.76 % complete ) and 2492 restraints for refining 1541 atoms. 1567 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3026 (Rfree = 0.000) for 1541 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 22: After refmac, R = 0.2947 (Rfree = 0.000) for 1516 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 23: After refmac, R = 0.2452 (Rfree = 0.000) for 1503 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 24: After refmac, R = 0.2687 (Rfree = 0.000) for 1498 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 25: After refmac, R = 0.2299 (Rfree = 0.000) for 1496 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 1546 seeds are put forward Round 1: 149 peptides, 13 chains. Longest chain 34 peptides. Score 0.630 Round 2: 155 peptides, 14 chains. Longest chain 31 peptides. Score 0.634 Round 3: 150 peptides, 14 chains. Longest chain 27 peptides. Score 0.617 Round 4: 143 peptides, 14 chains. Longest chain 32 peptides. Score 0.593 Round 5: 154 peptides, 14 chains. Longest chain 39 peptides. Score 0.630 Taking the results from Round 2 Chains 14, Residues 141, Estimated correctness of the model 39.4 % 2 chains (52 residues) have been docked in sequence ------------------------------------------------------ 5424 reflections ( 99.76 % complete ) and 2718 restraints for refining 1513 atoms. 1952 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2616 (Rfree = 0.000) for 1513 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 27: After refmac, R = 0.2350 (Rfree = 0.000) for 1493 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 28: After refmac, R = 0.2504 (Rfree = 0.000) for 1491 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 29: After refmac, R = 0.2331 (Rfree = 0.000) for 1485 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2192 (Rfree = 0.000) for 1483 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.38 2.63 Search for helices and strands: 0 residues in 0 chains, 1537 seeds are put forward Round 1: 141 peptides, 13 chains. Longest chain 27 peptides. Score 0.603 Round 2: 152 peptides, 12 chains. Longest chain 31 peptides. Score 0.655 Round 3: 157 peptides, 12 chains. Longest chain 34 peptides. Score 0.671 Round 4: 154 peptides, 13 chains. Longest chain 25 peptides. Score 0.646 Round 5: 159 peptides, 13 chains. Longest chain 32 peptides. Score 0.662 Taking the results from Round 3 Chains 15, Residues 145, Estimated correctness of the model 50.1 % 3 chains (69 residues) have been docked in sequence ------------------------------------------------------ 5424 reflections ( 99.76 % complete ) and 2500 restraints for refining 1513 atoms. 1634 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2446 (Rfree = 0.000) for 1513 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 32: After refmac, R = 0.2528 (Rfree = 0.000) for 1503 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 33: After refmac, R = 0.2412 (Rfree = 0.000) for 1493 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.2115 (Rfree = 0.000) for 1490 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 35: After refmac, R = 0.1970 (Rfree = 0.000) for 1491 atoms. Found 4 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 2.58 Search for helices and strands: 0 residues in 0 chains, 1542 seeds are put forward Round 1: 148 peptides, 15 chains. Longest chain 25 peptides. Score 0.594 Round 2: 160 peptides, 12 chains. Longest chain 49 peptides. Score 0.680 Round 3: 156 peptides, 11 chains. Longest chain 54 peptides. Score 0.683 Round 4: 155 peptides, 13 chains. Longest chain 37 peptides. Score 0.649 Round 5: 158 peptides, 14 chains. Longest chain 34 peptides. Score 0.643 Taking the results from Round 3 Chains 14, Residues 145, Estimated correctness of the model 53.4 % 3 chains (65 residues) have been docked in sequence ------------------------------------------------------ 5424 reflections ( 99.76 % complete ) and 2562 restraints for refining 1513 atoms. 1707 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2634 (Rfree = 0.000) for 1513 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 37: After refmac, R = 0.2395 (Rfree = 0.000) for 1496 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 38: After refmac, R = 0.2572 (Rfree = 0.000) for 1492 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2146 (Rfree = 0.000) for 1492 atoms. Found 8 (10 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2151 (Rfree = 0.000) for 1488 atoms. Found 7 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 2.61 Search for helices and strands: 0 residues in 0 chains, 1523 seeds are put forward Round 1: 142 peptides, 14 chains. Longest chain 34 peptides. Score 0.589 Round 2: 147 peptides, 10 chains. Longest chain 31 peptides. Score 0.671 Round 3: 155 peptides, 11 chains. Longest chain 32 peptides. Score 0.680 Round 4: 162 peptides, 13 chains. Longest chain 27 peptides. Score 0.671 Round 5: 155 peptides, 12 chains. Longest chain 46 peptides. Score 0.665 Taking the results from Round 3 Chains 13, Residues 144, Estimated correctness of the model 52.6 % 3 chains (63 residues) have been docked in sequence ------------------------------------------------------ 5424 reflections ( 99.76 % complete ) and 2596 restraints for refining 1513 atoms. 1772 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2439 (Rfree = 0.000) for 1513 atoms. Found 9 (10 requested) and removed 13 (5 requested) atoms. Cycle 42: After refmac, R = 0.2668 (Rfree = 0.000) for 1499 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 43: After refmac, R = 0.2638 (Rfree = 0.000) for 1493 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 44: After refmac, R = 0.2717 (Rfree = 0.000) for 1489 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 45: After refmac, R = 0.2639 (Rfree = 0.000) for 1484 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 2.66 Search for helices and strands: 0 residues in 0 chains, 1514 seeds are put forward Round 1: 133 peptides, 12 chains. Longest chain 31 peptides. Score 0.592 Round 2: 138 peptides, 12 chains. Longest chain 32 peptides. Score 0.609 Round 3: 140 peptides, 12 chains. Longest chain 32 peptides. Score 0.616 Round 4: 144 peptides, 11 chains. Longest chain 34 peptides. Score 0.646 Round 5: 134 peptides, 13 chains. Longest chain 32 peptides. Score 0.578 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 133, Estimated correctness of the model 43.0 % 3 chains (50 residues) have been docked in sequence Sequence coverage is 37 % Consider running further cycles of model building using 2gm6-3_warpNtrace.pdb as input Building loops using Loopy2018 14 chains (133 residues) following loop building 3 chains (50 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5424 reflections ( 99.76 % complete ) and 2806 restraints for refining 1513 atoms. 2067 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2772 (Rfree = 0.000) for 1513 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2715 (Rfree = 0.000) for 1499 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2883 (Rfree = 0.000) for 1484 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2367 (Rfree = 0.000) for 1472 atoms. TimeTaking 43.45