null Sun 23 Dec 22:23:02 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 2ia7-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ia7-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-1.7-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/2ia7-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-1.7-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 22:23:12 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/2ia7-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ia7-1.7-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 115 and 0 Target number of residues in the AU: 115 Target solvent content: 0.4482 Checking the provided sequence file Detected sequence length: 134 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 134 Adjusted target solvent content: 0.36 Input MTZ file: 2ia7-1.7-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: 19 Cell parameters: 40.240 43.350 64.660 90.000 90.000 90.000 Input sequence file: 2ia7-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 1072 target number of atoms Had to go as low as 0.45 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 1 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: 26.833 1.651 Wilson plot Bfac: 13.66 13899 reflections ( 98.38 % complete ) and 0 restraints for refining 1180 atoms. Observations/parameters ratio is 2.94 ------------------------------------------------------ Starting model: R = 0.4034 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3518 (Rfree = 0.000) for 1180 atoms. Found 50 (69 requested) and removed 45 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.91 2.31 Round 1: 52 peptides, 8 chains. Longest chain 15 peptides. Score 0.473 Round 2: 56 peptides, 6 chains. Longest chain 17 peptides. Score 0.624 Round 3: 62 peptides, 7 chains. Longest chain 19 peptides. Score 0.638 Round 4: 63 peptides, 6 chains. Longest chain 22 peptides. Score 0.690 Round 5: 65 peptides, 7 chains. Longest chain 23 peptides. Score 0.666 Taking the results from Round 4 Chains 6, Residues 57, Estimated correctness of the model 95.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 13899 reflections ( 98.38 % complete ) and 2312 restraints for refining 1074 atoms. 2090 conditional restraints added. Observations/parameters ratio is 3.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3719 (Rfree = 0.000) for 1074 atoms. Found 55 (63 requested) and removed 33 (31 requested) atoms. Cycle 2: After refmac, R = 0.3480 (Rfree = 0.000) for 1094 atoms. Found 45 (64 requested) and removed 32 (32 requested) atoms. Cycle 3: After refmac, R = 0.3258 (Rfree = 0.000) for 1106 atoms. Found 41 (65 requested) and removed 16 (32 requested) atoms. Cycle 4: After refmac, R = 0.3073 (Rfree = 0.000) for 1129 atoms. Found 36 (66 requested) and removed 7 (33 requested) atoms. Cycle 5: After refmac, R = 0.2969 (Rfree = 0.000) for 1154 atoms. Found 26 (68 requested) and removed 7 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.66 2.01 Round 1: 63 peptides, 7 chains. Longest chain 22 peptides. Score 0.648 Round 2: 66 peptides, 6 chains. Longest chain 22 peptides. Score 0.715 Round 3: 70 peptides, 4 chains. Longest chain 26 peptides. Score 0.811 Round 4: 73 peptides, 5 chains. Longest chain 22 peptides. Score 0.798 Round 5: 74 peptides, 4 chains. Longest chain 26 peptides. Score 0.832 Taking the results from Round 5 Chains 5, Residues 70, Estimated correctness of the model 98.5 % 2 chains (43 residues) have been docked in sequence Building loops using Loopy2018 5 chains (70 residues) following loop building 2 chains (43 residues) in sequence following loop building ------------------------------------------------------ 13899 reflections ( 98.38 % complete ) and 1792 restraints for refining 1150 atoms. 1306 conditional restraints added. Observations/parameters ratio is 3.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3303 (Rfree = 0.000) for 1150 atoms. Found 48 (68 requested) and removed 18 (34 requested) atoms. Cycle 7: After refmac, R = 0.3134 (Rfree = 0.000) for 1180 atoms. Found 39 (69 requested) and removed 7 (34 requested) atoms. Cycle 8: After refmac, R = 0.2997 (Rfree = 0.000) for 1206 atoms. Found 42 (71 requested) and removed 5 (35 requested) atoms. Cycle 9: After refmac, R = 0.2899 (Rfree = 0.000) for 1240 atoms. Found 32 (73 requested) and removed 10 (36 requested) atoms. Cycle 10: After refmac, R = 0.2883 (Rfree = 0.000) for 1260 atoms. Found 32 (74 requested) and removed 2 (37 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.68 2.03 Round 1: 80 peptides, 7 chains. Longest chain 26 peptides. Score 0.780 Round 2: 68 peptides, 6 chains. Longest chain 22 peptides. Score 0.731 Round 3: 77 peptides, 5 chains. Longest chain 26 peptides. Score 0.820 Round 4: 77 peptides, 5 chains. Longest chain 26 peptides. Score 0.820 Round 5: 78 peptides, 6 chains. Longest chain 26 peptides. Score 0.798 Taking the results from Round 4 Chains 6, Residues 72, Estimated correctness of the model 98.3 % 2 chains (44 residues) have been docked in sequence Building loops using Loopy2018 6 chains (72 residues) following loop building 2 chains (44 residues) in sequence following loop building ------------------------------------------------------ 13899 reflections ( 98.38 % complete ) and 1901 restraints for refining 1218 atoms. 1404 conditional restraints added. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3119 (Rfree = 0.000) for 1218 atoms. Found 57 (72 requested) and removed 22 (36 requested) atoms. Cycle 12: After refmac, R = 0.2977 (Rfree = 0.000) for 1252 atoms. Found 34 (74 requested) and removed 3 (37 requested) atoms. Cycle 13: After refmac, R = 0.2928 (Rfree = 0.000) for 1279 atoms. Found 32 (75 requested) and removed 4 (37 requested) atoms. Cycle 14: After refmac, R = 0.2830 (Rfree = 0.000) for 1307 atoms. Found 33 (77 requested) and removed 6 (38 requested) atoms. Cycle 15: After refmac, R = 0.2825 (Rfree = 0.000) for 1333 atoms. Found 35 (78 requested) and removed 4 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.65 2.00 Round 1: 71 peptides, 5 chains. Longest chain 26 peptides. Score 0.786 Round 2: 72 peptides, 4 chains. Longest chain 26 peptides. Score 0.822 Round 3: 75 peptides, 6 chains. Longest chain 22 peptides. Score 0.780 Round 4: 71 peptides, 7 chains. Longest chain 22 peptides. Score 0.717 Round 5: 64 peptides, 5 chains. Longest chain 26 peptides. Score 0.738 Taking the results from Round 2 Chains 6, Residues 68, Estimated correctness of the model 98.4 % 2 chains (33 residues) have been docked in sequence Building loops using Loopy2018 6 chains (68 residues) following loop building 2 chains (33 residues) in sequence following loop building ------------------------------------------------------ 13899 reflections ( 98.38 % complete ) and 2399 restraints for refining 1293 atoms. 2007 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2971 (Rfree = 0.000) for 1293 atoms. Found 51 (76 requested) and removed 8 (38 requested) atoms. Cycle 17: After refmac, R = 0.2883 (Rfree = 0.000) for 1336 atoms. Found 31 (79 requested) and removed 3 (39 requested) atoms. Cycle 18: After refmac, R = 0.2811 (Rfree = 0.000) for 1361 atoms. Found 31 (80 requested) and removed 9 (40 requested) atoms. Cycle 19: After refmac, R = 0.2766 (Rfree = 0.000) for 1383 atoms. Found 31 (81 requested) and removed 11 (40 requested) atoms. Cycle 20: After refmac, R = 0.2740 (Rfree = 0.000) for 1401 atoms. Found 33 (83 requested) and removed 13 (41 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.63 1.97 Round 1: 72 peptides, 5 chains. Longest chain 26 peptides. Score 0.792 Round 2: 76 peptides, 5 chains. Longest chain 26 peptides. Score 0.815 Round 3: 78 peptides, 4 chains. Longest chain 48 peptides. Score 0.851 Round 4: 77 peptides, 6 chains. Longest chain 22 peptides. Score 0.792 Round 5: 72 peptides, 6 chains. Longest chain 22 peptides. Score 0.760 Taking the results from Round 3 Chains 5, Residues 74, Estimated correctness of the model 98.8 % 2 chains (40 residues) have been docked in sequence Building loops using Loopy2018 5 chains (74 residues) following loop building 2 chains (40 residues) in sequence following loop building ------------------------------------------------------ 13899 reflections ( 98.38 % complete ) and 2428 restraints for refining 1335 atoms. 1979 conditional restraints added. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2980 (Rfree = 0.000) for 1335 atoms. Found 66 (78 requested) and removed 24 (39 requested) atoms. Cycle 22: After refmac, R = 0.2905 (Rfree = 0.000) for 1375 atoms. Found 42 (81 requested) and removed 7 (40 requested) atoms. Cycle 23: After refmac, R = 0.2769 (Rfree = 0.000) for 1408 atoms. Found 35 (83 requested) and removed 7 (41 requested) atoms. Cycle 24: After refmac, R = 0.2691 (Rfree = 0.000) for 1432 atoms. Found 35 (84 requested) and removed 6 (42 requested) atoms. Cycle 25: After refmac, R = 0.2638 (Rfree = 0.000) for 1458 atoms. Found 34 (86 requested) and removed 4 (43 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.63 1.97 Round 1: 71 peptides, 5 chains. Longest chain 26 peptides. Score 0.786 Round 2: 71 peptides, 3 chains. Longest chain 48 peptides. Score 0.844 Round 3: 68 peptides, 4 chains. Longest chain 26 peptides. Score 0.799 Round 4: 69 peptides, 3 chains. Longest chain 48 peptides. Score 0.835 Round 5: 72 peptides, 5 chains. Longest chain 26 peptides. Score 0.792 Taking the results from Round 2 Chains 5, Residues 68, Estimated correctness of the model 98.7 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 13899 reflections ( 98.38 % complete ) and 2738 restraints for refining 1395 atoms. 2343 conditional restraints added. Observations/parameters ratio is 2.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2892 (Rfree = 0.000) for 1395 atoms. Found 64 (82 requested) and removed 20 (41 requested) atoms. Cycle 27: After refmac, R = 0.2791 (Rfree = 0.000) for 1439 atoms. Found 29 (85 requested) and removed 13 (42 requested) atoms. Cycle 28: After refmac, R = 0.2645 (Rfree = 0.000) for 1455 atoms. Found 31 (86 requested) and removed 4 (43 requested) atoms. Cycle 29: After refmac, R = 0.2604 (Rfree = 0.000) for 1480 atoms. Found 28 (87 requested) and removed 7 (43 requested) atoms. Cycle 30: After refmac, R = 0.2580 (Rfree = 0.000) for 1500 atoms. Found 31 (88 requested) and removed 8 (44 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.63 1.97 Round 1: 64 peptides, 4 chains. Longest chain 25 peptides. Score 0.774 Round 2: 72 peptides, 6 chains. Longest chain 25 peptides. Score 0.760 Round 3: 74 peptides, 6 chains. Longest chain 25 peptides. Score 0.773 Round 4: 71 peptides, 5 chains. Longest chain 25 peptides. Score 0.786 Round 5: 67 peptides, 5 chains. Longest chain 25 peptides. Score 0.760 Taking the results from Round 4 Chains 6, Residues 66, Estimated correctness of the model 97.7 % 2 chains (43 residues) have been docked in sequence Building loops using Loopy2018 6 chains (66 residues) following loop building 2 chains (43 residues) in sequence following loop building ------------------------------------------------------ 13899 reflections ( 98.38 % complete ) and 2629 restraints for refining 1419 atoms. 2189 conditional restraints added. Observations/parameters ratio is 2.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2858 (Rfree = 0.000) for 1419 atoms. Found 78 (83 requested) and removed 20 (41 requested) atoms. Cycle 32: After refmac, R = 0.2733 (Rfree = 0.000) for 1475 atoms. Found 48 (87 requested) and removed 9 (43 requested) atoms. Cycle 33: After refmac, R = 0.2684 (Rfree = 0.000) for 1513 atoms. Found 43 (89 requested) and removed 11 (44 requested) atoms. Cycle 34: After refmac, R = 0.2598 (Rfree = 0.000) for 1542 atoms. Found 36 (91 requested) and removed 9 (45 requested) atoms. Cycle 35: After refmac, R = 0.2554 (Rfree = 0.000) for 1567 atoms. Found 33 (92 requested) and removed 11 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.63 1.97 Round 1: 71 peptides, 4 chains. Longest chain 25 peptides. Score 0.816 Round 2: 68 peptides, 4 chains. Longest chain 26 peptides. Score 0.799 Round 3: 72 peptides, 4 chains. Longest chain 25 peptides. Score 0.822 Round 4: 63 peptides, 3 chains. Longest chain 25 peptides. Score 0.801 Round 5: 70 peptides, 5 chains. Longest chain 26 peptides. Score 0.780 Taking the results from Round 3 Chains 5, Residues 68, Estimated correctness of the model 98.4 % 1 chains (23 residues) have been docked in sequence ------------------------------------------------------ 13899 reflections ( 98.38 % complete ) and 3014 restraints for refining 1487 atoms. 2630 conditional restraints added. Observations/parameters ratio is 2.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2729 (Rfree = 0.000) for 1487 atoms. Found 81 (87 requested) and removed 20 (43 requested) atoms. Cycle 37: After refmac, R = 0.2660 (Rfree = 0.000) for 1547 atoms. Found 36 (91 requested) and removed 11 (45 requested) atoms. Cycle 38: After refmac, R = 0.2498 (Rfree = 0.000) for 1571 atoms. Found 32 (93 requested) and removed 10 (46 requested) atoms. Cycle 39: After refmac, R = 0.2446 (Rfree = 0.000) for 1592 atoms. Found 47 (94 requested) and removed 10 (47 requested) atoms. Cycle 40: After refmac, R = 0.2440 (Rfree = 0.000) for 1625 atoms. Found 27 (96 requested) and removed 17 (48 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.63 1.97 Round 1: 69 peptides, 4 chains. Longest chain 26 peptides. Score 0.805 Round 2: 71 peptides, 4 chains. Longest chain 26 peptides. Score 0.816 Round 3: 69 peptides, 4 chains. Longest chain 26 peptides. Score 0.805 Round 4: 72 peptides, 4 chains. Longest chain 26 peptides. Score 0.822 Round 5: 68 peptides, 5 chains. Longest chain 26 peptides. Score 0.766 Taking the results from Round 4 Chains 6, Residues 68, Estimated correctness of the model 98.4 % 2 chains (38 residues) have been docked in sequence Building loops using Loopy2018 6 chains (68 residues) following loop building 2 chains (38 residues) in sequence following loop building ------------------------------------------------------ 13899 reflections ( 98.38 % complete ) and 2984 restraints for refining 1541 atoms. 2544 conditional restraints added. Observations/parameters ratio is 2.25 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2735 (Rfree = 0.000) for 1541 atoms. Found 72 (89 requested) and removed 21 (45 requested) atoms. Cycle 42: After refmac, R = 0.2667 (Rfree = 0.000) for 1590 atoms. Found 47 (92 requested) and removed 8 (47 requested) atoms. Cycle 43: After refmac, R = 0.2556 (Rfree = 0.000) for 1626 atoms. Found 38 (94 requested) and removed 11 (48 requested) atoms. Cycle 44: After refmac, R = 0.2472 (Rfree = 0.000) for 1653 atoms. Found 25 (95 requested) and removed 10 (48 requested) atoms. Cycle 45: After refmac, R = 0.2431 (Rfree = 0.000) for 1665 atoms. Found 44 (96 requested) and removed 12 (49 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.63 1.97 Round 1: 67 peptides, 4 chains. Longest chain 24 peptides. Score 0.793 Round 2: 67 peptides, 4 chains. Longest chain 25 peptides. Score 0.793 Round 3: 72 peptides, 4 chains. Longest chain 25 peptides. Score 0.822 Round 4: 67 peptides, 6 chains. Longest chain 21 peptides. Score 0.723 Round 5: 72 peptides, 4 chains. Longest chain 25 peptides. Score 0.822 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 68, Estimated correctness of the model 98.4 % 2 chains (41 residues) have been docked in sequence Sequence coverage is 59 % Consider running further cycles of model building using 2ia7-1_warpNtrace.pdb as input Building loops using Loopy2018 5 chains (68 residues) following loop building 2 chains (41 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13899 reflections ( 98.38 % complete ) and 3108 restraints for refining 1554 atoms. 2664 conditional restraints added. Observations/parameters ratio is 2.24 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2732 (Rfree = 0.000) for 1554 atoms. Found 0 (89 requested) and removed 0 (45 requested) atoms. Cycle 47: After refmac, R = 0.2615 (Rfree = 0.000) for 1551 atoms. Found 0 (89 requested) and removed 0 (45 requested) atoms. Cycle 48: After refmac, R = 0.2564 (Rfree = 0.000) for 1550 atoms. Found 0 (89 requested) and removed 0 (45 requested) atoms. Cycle 49: After refmac, R = 0.2536 (Rfree = 0.000) for 1550 atoms. Found 0 (89 requested) and removed 0 (45 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:51 GMT 2018 Job finished. TimeTaking 27.83 Used memory is bytes: 4682256