Mon 24 Dec 01:10:09 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pg4-2.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-2.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pg4-2.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-2.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-2.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-2.2-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 01:10:14 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-2.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pg4-2.2-parrot-mrncs/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 175 and 0 Target number of residues in the AU: 175 Target solvent content: 0.5729 Checking the provided sequence file Detected sequence length: 95 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 190 Adjusted target solvent content: 0.54 Input MTZ file: 2pg4-2.2-parrot-mrncs.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: 90 Cell parameters: 109.840 109.840 36.760 90.000 90.000 90.000 Input sequence file: 2pg4-2.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 1520 target number of atoms Had to go as low as 0.65 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 77.669 2.195 Wilson plot Bfac: 42.55 11724 reflections ( 98.80 % complete ) and 0 restraints for refining 1682 atoms. Observations/parameters ratio is 1.74 ------------------------------------------------------ Starting model: R = 0.3935 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3672 (Rfree = 0.000) for 1682 atoms. Found 19 (44 requested) and removed 32 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.76 2.62 NCS extension: 0 residues added, 1669 seeds are put forward Round 1: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.423 Round 2: 109 peptides, 16 chains. Longest chain 24 peptides. Score 0.510 Round 3: 126 peptides, 15 chains. Longest chain 27 peptides. Score 0.631 Round 4: 132 peptides, 16 chains. Longest chain 18 peptides. Score 0.638 Round 5: 132 peptides, 15 chains. Longest chain 33 peptides. Score 0.660 Taking the results from Round 5 Chains 16, Residues 117, Estimated correctness of the model 86.7 % 1 chains (30 residues) have been docked in sequence ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2650 restraints for refining 1452 atoms. 2066 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3943 (Rfree = 0.000) for 1452 atoms. Found 12 (38 requested) and removed 22 (19 requested) atoms. Cycle 2: After refmac, R = 0.3737 (Rfree = 0.000) for 1437 atoms. Found 13 (37 requested) and removed 18 (18 requested) atoms. Cycle 3: After refmac, R = 0.3629 (Rfree = 0.000) for 1423 atoms. Found 8 (37 requested) and removed 18 (18 requested) atoms. Cycle 4: After refmac, R = 0.3555 (Rfree = 0.000) for 1400 atoms. Found 12 (37 requested) and removed 18 (18 requested) atoms. Cycle 5: After refmac, R = 0.3510 (Rfree = 0.000) for 1390 atoms. Found 10 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.57 2.44 NCS extension: 43 residues added (4 deleted due to clashes), 1429 seeds are put forward Round 1: 128 peptides, 13 chains. Longest chain 30 peptides. Score 0.684 Round 2: 135 peptides, 14 chains. Longest chain 36 peptides. Score 0.694 Round 3: 138 peptides, 11 chains. Longest chain 33 peptides. Score 0.762 Round 4: 135 peptides, 13 chains. Longest chain 24 peptides. Score 0.714 Round 5: 137 peptides, 10 chains. Longest chain 41 peptides. Score 0.775 Taking the results from Round 5 Chains 10, Residues 127, Estimated correctness of the model 93.8 % 1 chains (40 residues) have been docked in sequence ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2631 restraints for refining 1439 atoms. 1969 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3746 (Rfree = 0.000) for 1439 atoms. Found 29 (37 requested) and removed 18 (18 requested) atoms. Cycle 7: After refmac, R = 0.3557 (Rfree = 0.000) for 1445 atoms. Found 23 (37 requested) and removed 20 (19 requested) atoms. Cycle 8: After refmac, R = 0.3376 (Rfree = 0.000) for 1441 atoms. Found 7 (36 requested) and removed 19 (19 requested) atoms. Cycle 9: After refmac, R = 0.3392 (Rfree = 0.000) for 1422 atoms. Found 10 (35 requested) and removed 18 (18 requested) atoms. Cycle 10: After refmac, R = 0.3326 (Rfree = 0.000) for 1413 atoms. Found 16 (34 requested) and removed 17 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.55 2.42 NCS extension: 32 residues added (3 deleted due to clashes), 1444 seeds are put forward Round 1: 142 peptides, 14 chains. Longest chain 25 peptides. Score 0.723 Round 2: 134 peptides, 12 chains. Longest chain 27 peptides. Score 0.729 Round 3: 140 peptides, 11 chains. Longest chain 36 peptides. Score 0.769 Round 4: 140 peptides, 9 chains. Longest chain 36 peptides. Score 0.801 Round 5: 133 peptides, 13 chains. Longest chain 28 peptides. Score 0.706 Taking the results from Round 4 Chains 9, Residues 131, Estimated correctness of the model 95.0 % 2 chains (68 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 46 A 8 chains (136 residues) following loop building 1 chains (73 residues) in sequence following loop building ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2203 restraints for refining 1452 atoms. 1360 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3522 (Rfree = 0.000) for 1452 atoms. Found 27 (34 requested) and removed 21 (19 requested) atoms. Cycle 12: After refmac, R = 0.3389 (Rfree = 0.000) for 1454 atoms. Found 17 (33 requested) and removed 19 (19 requested) atoms. Cycle 13: After refmac, R = 0.3315 (Rfree = 0.000) for 1449 atoms. Found 15 (33 requested) and removed 19 (19 requested) atoms. Cycle 14: After refmac, R = 0.3255 (Rfree = 0.000) for 1444 atoms. Found 11 (31 requested) and removed 18 (18 requested) atoms. Cycle 15: After refmac, R = 0.3185 (Rfree = 0.000) for 1436 atoms. Found 13 (30 requested) and removed 15 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.54 2.41 NCS extension: 87 residues added (28 deleted due to clashes), 1523 seeds are put forward Round 1: 129 peptides, 15 chains. Longest chain 20 peptides. Score 0.646 Round 2: 134 peptides, 8 chains. Longest chain 74 peptides. Score 0.799 Round 3: 130 peptides, 11 chains. Longest chain 51 peptides. Score 0.732 Round 4: 125 peptides, 11 chains. Longest chain 32 peptides. Score 0.712 Round 5: 132 peptides, 8 chains. Longest chain 59 peptides. Score 0.792 Taking the results from Round 2 Chains 8, Residues 126, Estimated correctness of the model 94.9 % 1 chains (73 residues) have been docked in sequence ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2242 restraints for refining 1452 atoms. 1439 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3233 (Rfree = 0.000) for 1452 atoms. Found 16 (30 requested) and removed 19 (19 requested) atoms. Cycle 17: After refmac, R = 0.3101 (Rfree = 0.000) for 1447 atoms. Found 9 (30 requested) and removed 19 (19 requested) atoms. Cycle 18: After refmac, R = 0.3022 (Rfree = 0.000) for 1436 atoms. Found 11 (28 requested) and removed 10 (18 requested) atoms. Cycle 19: After refmac, R = 0.2975 (Rfree = 0.000) for 1434 atoms. Found 14 (27 requested) and removed 12 (18 requested) atoms. Cycle 20: After refmac, R = 0.2967 (Rfree = 0.000) for 1435 atoms. Found 9 (27 requested) and removed 7 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.54 2.41 NCS extension: 73 residues added (22 deleted due to clashes), 1512 seeds are put forward Round 1: 137 peptides, 8 chains. Longest chain 44 peptides. Score 0.807 Round 2: 131 peptides, 8 chains. Longest chain 37 peptides. Score 0.789 Round 3: 139 peptides, 8 chains. Longest chain 72 peptides. Score 0.813 Round 4: 131 peptides, 10 chains. Longest chain 28 peptides. Score 0.755 Round 5: 141 peptides, 7 chains. Longest chain 72 peptides. Score 0.833 Taking the results from Round 5 Chains 7, Residues 134, Estimated correctness of the model 96.4 % 1 chains (71 residues) have been docked in sequence ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2154 restraints for refining 1452 atoms. 1326 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3103 (Rfree = 0.000) for 1452 atoms. Found 23 (27 requested) and removed 19 (19 requested) atoms. Cycle 22: After refmac, R = 0.2945 (Rfree = 0.000) for 1454 atoms. Found 14 (26 requested) and removed 10 (19 requested) atoms. Cycle 23: After refmac, R = 0.2870 (Rfree = 0.000) for 1458 atoms. Found 12 (25 requested) and removed 12 (19 requested) atoms. Cycle 24: After refmac, R = 0.2798 (Rfree = 0.000) for 1458 atoms. Found 14 (24 requested) and removed 9 (19 requested) atoms. Cycle 25: After refmac, R = 0.2790 (Rfree = 0.000) for 1462 atoms. Found 13 (24 requested) and removed 9 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.53 2.40 NCS extension: 78 residues added (38 deleted due to clashes), 1546 seeds are put forward Round 1: 141 peptides, 7 chains. Longest chain 71 peptides. Score 0.833 Round 2: 146 peptides, 10 chains. Longest chain 62 peptides. Score 0.803 Round 3: 148 peptides, 9 chains. Longest chain 37 peptides. Score 0.823 Round 4: 142 peptides, 10 chains. Longest chain 41 peptides. Score 0.791 Round 5: 137 peptides, 10 chains. Longest chain 37 peptides. Score 0.775 Taking the results from Round 1 Chains 7, Residues 134, Estimated correctness of the model 96.4 % 1 chains (70 residues) have been docked in sequence ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2187 restraints for refining 1452 atoms. 1363 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2890 (Rfree = 0.000) for 1452 atoms. Found 17 (23 requested) and removed 17 (19 requested) atoms. Cycle 27: After refmac, R = 0.2792 (Rfree = 0.000) for 1451 atoms. Found 11 (22 requested) and removed 6 (19 requested) atoms. Cycle 28: After refmac, R = 0.2733 (Rfree = 0.000) for 1455 atoms. Found 5 (21 requested) and removed 0 (19 requested) atoms. Cycle 29: After refmac, R = 0.2710 (Rfree = 0.000) for 1459 atoms. Found 4 (21 requested) and removed 3 (19 requested) atoms. Cycle 30: After refmac, R = 0.2713 (Rfree = 0.000) for 1460 atoms. Found 4 (21 requested) and removed 2 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.51 2.38 NCS extension: 46 residues added (47 deleted due to clashes), 1509 seeds are put forward Round 1: 143 peptides, 7 chains. Longest chain 71 peptides. Score 0.838 Round 2: 142 peptides, 9 chains. Longest chain 33 peptides. Score 0.807 Round 3: 142 peptides, 9 chains. Longest chain 43 peptides. Score 0.807 Round 4: 144 peptides, 11 chains. Longest chain 34 peptides. Score 0.782 Round 5: 135 peptides, 11 chains. Longest chain 23 peptides. Score 0.751 Taking the results from Round 1 Chains 7, Residues 136, Estimated correctness of the model 96.6 % 1 chains (70 residues) have been docked in sequence ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2124 restraints for refining 1452 atoms. 1292 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2806 (Rfree = 0.000) for 1452 atoms. Found 20 (21 requested) and removed 16 (19 requested) atoms. Cycle 32: After refmac, R = 0.2733 (Rfree = 0.000) for 1455 atoms. Found 5 (20 requested) and removed 5 (19 requested) atoms. Cycle 33: After refmac, R = 0.2658 (Rfree = 0.000) for 1454 atoms. Found 7 (19 requested) and removed 2 (19 requested) atoms. Cycle 34: After refmac, R = 0.2667 (Rfree = 0.000) for 1459 atoms. Found 2 (19 requested) and removed 3 (19 requested) atoms. Cycle 35: After refmac, R = 0.2650 (Rfree = 0.000) for 1457 atoms. Found 9 (19 requested) and removed 3 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.51 2.38 NCS extension: 44 residues added (67 deleted due to clashes), 1507 seeds are put forward Round 1: 144 peptides, 8 chains. Longest chain 37 peptides. Score 0.827 Round 2: 147 peptides, 7 chains. Longest chain 62 peptides. Score 0.848 Round 3: 153 peptides, 6 chains. Longest chain 72 peptides. Score 0.873 Round 4: 153 peptides, 6 chains. Longest chain 54 peptides. Score 0.873 Round 5: 150 peptides, 9 chains. Longest chain 29 peptides. Score 0.829 Taking the results from Round 4 Chains 6, Residues 147, Estimated correctness of the model 97.8 % 1 chains (53 residues) have been docked in sequence ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2250 restraints for refining 1452 atoms. 1448 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2905 (Rfree = 0.000) for 1452 atoms. Found 18 (19 requested) and removed 13 (19 requested) atoms. Cycle 37: After refmac, R = 0.2804 (Rfree = 0.000) for 1457 atoms. Found 15 (19 requested) and removed 5 (19 requested) atoms. Cycle 38: After refmac, R = 0.2727 (Rfree = 0.000) for 1467 atoms. Found 8 (19 requested) and removed 3 (19 requested) atoms. Cycle 39: After refmac, R = 0.2701 (Rfree = 0.000) for 1472 atoms. Found 5 (19 requested) and removed 7 (19 requested) atoms. Cycle 40: After refmac, R = 0.2681 (Rfree = 0.000) for 1470 atoms. Found 4 (19 requested) and removed 2 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.51 2.38 NCS extension: 15 residues added (16 deleted due to clashes), 1488 seeds are put forward Round 1: 148 peptides, 7 chains. Longest chain 71 peptides. Score 0.850 Round 2: 151 peptides, 8 chains. Longest chain 61 peptides. Score 0.844 Round 3: 148 peptides, 7 chains. Longest chain 72 peptides. Score 0.850 Round 4: 151 peptides, 10 chains. Longest chain 51 peptides. Score 0.817 Round 5: 152 peptides, 9 chains. Longest chain 37 peptides. Score 0.834 Taking the results from Round 3 Chains 8, Residues 141, Estimated correctness of the model 97.0 % 2 chains (90 residues) have been docked in sequence Building loops using Loopy2018 8 chains (141 residues) following loop building 2 chains (90 residues) in sequence following loop building ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 1948 restraints for refining 1459 atoms. 1021 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2889 (Rfree = 0.000) for 1459 atoms. Found 19 (19 requested) and removed 19 (19 requested) atoms. Cycle 42: After refmac, R = 0.2792 (Rfree = 0.000) for 1459 atoms. Found 9 (19 requested) and removed 12 (19 requested) atoms. Cycle 43: After refmac, R = 0.2701 (Rfree = 0.000) for 1456 atoms. Found 8 (19 requested) and removed 5 (19 requested) atoms. Cycle 44: After refmac, R = 0.2663 (Rfree = 0.000) for 1458 atoms. Found 5 (19 requested) and removed 6 (19 requested) atoms. Cycle 45: After refmac, R = 0.2647 (Rfree = 0.000) for 1457 atoms. Found 1 (19 requested) and removed 2 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.50 2.37 NCS extension: 42 residues added (55 deleted due to clashes), 1498 seeds are put forward Round 1: 156 peptides, 8 chains. Longest chain 61 peptides. Score 0.856 Round 2: 155 peptides, 9 chains. Longest chain 38 peptides. Score 0.841 Round 3: 154 peptides, 8 chains. Longest chain 61 peptides. Score 0.851 Round 4: 157 peptides, 7 chains. Longest chain 38 peptides. Score 0.870 Round 5: 153 peptides, 10 chains. Longest chain 29 peptides. Score 0.823 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 7, Residues 150, Estimated correctness of the model 97.7 % 3 chains (101 residues) have been docked in sequence Sequence coverage is 66 % Consider running further cycles of model building using 2pg4-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 39 A and 42 A 6 chains (152 residues) following loop building 2 chains (103 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11724 reflections ( 98.80 % complete ) and 1787 restraints for refining 1466 atoms. 760 conditional restraints added. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2934 (Rfree = 0.000) for 1466 atoms. Found 0 (19 requested) and removed 8 (19 requested) atoms. Cycle 47: After refmac, R = 0.2819 (Rfree = 0.000) for 1457 atoms. Found 0 (19 requested) and removed 2 (19 requested) atoms. Cycle 48: After refmac, R = 0.2768 (Rfree = 0.000) for 1455 atoms. Found 0 (19 requested) and removed 2 (19 requested) atoms. Cycle 49: After refmac, R = 0.2734 (Rfree = 0.000) for 1452 atoms. TimeTaking 25.82