Mon 24 Dec 01:07:31 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 2prr-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prr-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-4.0-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/2prr-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-4.0-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 01:07:35 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/2prr-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prr-4.0-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 1687 and 0 Target number of residues in the AU: 1687 Target solvent content: 0.6799 Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 2364 Adjusted target solvent content: 0.55 Input MTZ file: 2prr-4.0-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: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.85 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 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: 119.307 4.000 Wilson plot Bfac: 101.00 22829 reflections ( 97.72 % complete ) and 0 restraints for refining 20979 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3268 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2940 (Rfree = 0.000) for 20979 atoms. Found 99 (99 requested) and removed 136 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.97 3.71 Search for helices and strands: 0 residues in 0 chains, 21585 seeds are put forward NCS extension: 0 residues added, 21585 seeds are put forward Round 1: 937 peptides, 174 chains. Longest chain 13 peptides. Score 0.329 Round 2: 1116 peptides, 159 chains. Longest chain 22 peptides. Score 0.470 Round 3: 1166 peptides, 152 chains. Longest chain 24 peptides. Score 0.511 Round 4: 1220 peptides, 151 chains. Longest chain 24 peptides. Score 0.540 Round 5: 1229 peptides, 148 chains. Longest chain 25 peptides. Score 0.551 Taking the results from Round 5 Chains 152, Residues 1081, Estimated correctness of the model 0.0 % 6 chains (74 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39366 restraints for refining 17074 atoms. 34908 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2149 (Rfree = 0.000) for 17074 atoms. Found 39 (81 requested) and removed 104 (40 requested) atoms. Cycle 2: After refmac, R = 0.2014 (Rfree = 0.000) for 16765 atoms. Found 48 (80 requested) and removed 90 (40 requested) atoms. Cycle 3: After refmac, R = 0.1930 (Rfree = 0.000) for 16606 atoms. Found 33 (79 requested) and removed 96 (39 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1592 (Rfree = 0.000) for 16460 atoms. Found 18 (78 requested) and removed 59 (39 requested) atoms. Cycle 5: After refmac, R = 0.1527 (Rfree = 0.000) for 16389 atoms. Found 6 (78 requested) and removed 58 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.93 3.68 Search for helices and strands: 0 residues in 0 chains, 17126 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 17148 seeds are put forward Round 1: 1030 peptides, 175 chains. Longest chain 13 peptides. Score 0.383 Round 2: 1164 peptides, 156 chains. Longest chain 20 peptides. Score 0.501 Round 3: 1163 peptides, 150 chains. Longest chain 31 peptides. Score 0.514 Round 4: 1179 peptides, 151 chains. Longest chain 20 peptides. Score 0.520 Round 5: 1179 peptides, 150 chains. Longest chain 28 peptides. Score 0.522 Taking the results from Round 5 Chains 151, Residues 1029, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39648 restraints for refining 17075 atoms. 35599 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2035 (Rfree = 0.000) for 17075 atoms. Found 33 (81 requested) and removed 125 (40 requested) atoms. Cycle 7: After refmac, R = 0.2005 (Rfree = 0.000) for 16833 atoms. Found 64 (80 requested) and removed 103 (40 requested) atoms. Cycle 8: After refmac, R = 0.1878 (Rfree = 0.000) for 16702 atoms. Found 37 (79 requested) and removed 78 (39 requested) atoms. Cycle 9: After refmac, R = 0.1807 (Rfree = 0.000) for 16573 atoms. Found 48 (79 requested) and removed 74 (39 requested) atoms. Cycle 10: After refmac, R = 0.1743 (Rfree = 0.000) for 16480 atoms. Found 41 (78 requested) and removed 78 (39 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.91 3.66 Search for helices and strands: 0 residues in 0 chains, 17244 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 17270 seeds are put forward Round 1: 1023 peptides, 180 chains. Longest chain 15 peptides. Score 0.366 Round 2: 1127 peptides, 170 chains. Longest chain 14 peptides. Score 0.449 Round 3: 1164 peptides, 165 chains. Longest chain 21 peptides. Score 0.481 Round 4: 1174 peptides, 156 chains. Longest chain 22 peptides. Score 0.506 Round 5: 1172 peptides, 157 chains. Longest chain 22 peptides. Score 0.503 Taking the results from Round 4 Chains 158, Residues 1018, Estimated correctness of the model 0.0 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 38966 restraints for refining 17073 atoms. 34935 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1868 (Rfree = 0.000) for 17073 atoms. Found 49 (81 requested) and removed 117 (40 requested) atoms. Cycle 12: After refmac, R = 0.1793 (Rfree = 0.000) for 16852 atoms. Found 43 (80 requested) and removed 87 (40 requested) atoms. Cycle 13: After refmac, R = 0.1641 (Rfree = 0.000) for 16727 atoms. Found 30 (79 requested) and removed 83 (39 requested) atoms. Cycle 14: After refmac, R = 0.1654 (Rfree = 0.000) for 16622 atoms. Found 43 (79 requested) and removed 72 (39 requested) atoms. Cycle 15: After refmac, R = 0.1630 (Rfree = 0.000) for 16556 atoms. Found 38 (78 requested) and removed 65 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.91 3.66 Search for helices and strands: 0 residues in 0 chains, 17200 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 17218 seeds are put forward Round 1: 993 peptides, 184 chains. Longest chain 14 peptides. Score 0.337 Round 2: 1085 peptides, 164 chains. Longest chain 17 peptides. Score 0.441 Round 3: 1109 peptides, 167 chains. Longest chain 17 peptides. Score 0.447 Round 4: 1117 peptides, 157 chains. Longest chain 17 peptides. Score 0.475 Round 5: 1133 peptides, 167 chains. Longest chain 25 peptides. Score 0.460 Taking the results from Round 4 Chains 159, Residues 960, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39576 restraints for refining 17072 atoms. 35799 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1865 (Rfree = 0.000) for 17072 atoms. Found 39 (81 requested) and removed 94 (40 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1810 (Rfree = 0.000) for 16899 atoms. Found 57 (80 requested) and removed 91 (40 requested) atoms. Cycle 18: After refmac, R = 0.1737 (Rfree = 0.000) for 16819 atoms. Found 35 (80 requested) and removed 78 (40 requested) atoms. Cycle 19: After refmac, R = 0.1334 (Rfree = 0.000) for 16744 atoms. Found 13 (79 requested) and removed 57 (39 requested) atoms. Cycle 20: After refmac, R = 0.1258 (Rfree = 0.000) for 16678 atoms. Found 5 (79 requested) and removed 46 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.91 3.66 Search for helices and strands: 0 residues in 0 chains, 17329 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 17349 seeds are put forward Round 1: 978 peptides, 185 chains. Longest chain 11 peptides. Score 0.326 Round 2: 1097 peptides, 171 chains. Longest chain 16 peptides. Score 0.431 Round 3: 1099 peptides, 166 chains. Longest chain 20 peptides. Score 0.444 Round 4: 1102 peptides, 168 chains. Longest chain 15 peptides. Score 0.441 Round 5: 1088 peptides, 158 chains. Longest chain 19 peptides. Score 0.457 Taking the results from Round 5 Chains 159, Residues 930, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39826 restraints for refining 17077 atoms. 36140 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1891 (Rfree = 0.000) for 17077 atoms. Found 51 (81 requested) and removed 88 (40 requested) atoms. Cycle 22: After refmac, R = 0.1797 (Rfree = 0.000) for 16942 atoms. Found 59 (80 requested) and removed 66 (40 requested) atoms. Cycle 23: After refmac, R = 0.1732 (Rfree = 0.000) for 16886 atoms. Found 42 (80 requested) and removed 82 (40 requested) atoms. Cycle 24: After refmac, R = 0.1334 (Rfree = 0.000) for 16802 atoms. Found 11 (80 requested) and removed 59 (40 requested) atoms. Cycle 25: After refmac, R = 0.1267 (Rfree = 0.000) for 16734 atoms. Found 7 (79 requested) and removed 51 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.93 3.68 Search for helices and strands: 0 residues in 0 chains, 17351 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 17363 seeds are put forward Round 1: 914 peptides, 171 chains. Longest chain 12 peptides. Score 0.323 Round 2: 1037 peptides, 162 chains. Longest chain 19 peptides. Score 0.419 Round 3: 1035 peptides, 162 chains. Longest chain 17 peptides. Score 0.418 Round 4: 1027 peptides, 157 chains. Longest chain 16 peptides. Score 0.426 Round 5: 1006 peptides, 150 chains. Longest chain 17 peptides. Score 0.432 Taking the results from Round 5 Chains 150, Residues 856, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 40506 restraints for refining 17077 atoms. 37209 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1887 (Rfree = 0.000) for 17077 atoms. Found 62 (81 requested) and removed 76 (40 requested) atoms. Cycle 27: After refmac, R = 0.1879 (Rfree = 0.000) for 16981 atoms. Found 81 (81 requested) and removed 69 (40 requested) atoms. Cycle 28: After refmac, R = 0.1831 (Rfree = 0.000) for 16936 atoms. Found 80 (80 requested) and removed 69 (40 requested) atoms. Cycle 29: After refmac, R = 0.1698 (Rfree = 0.000) for 16895 atoms. Found 61 (80 requested) and removed 63 (40 requested) atoms. Cycle 30: After refmac, R = 0.1242 (Rfree = 0.000) for 16855 atoms. Found 14 (80 requested) and removed 51 (40 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.90 3.65 Search for helices and strands: 0 residues in 0 chains, 17396 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 17409 seeds are put forward Round 1: 831 peptides, 169 chains. Longest chain 10 peptides. Score 0.275 Round 2: 968 peptides, 164 chains. Longest chain 16 peptides. Score 0.374 Round 3: 995 peptides, 164 chains. Longest chain 17 peptides. Score 0.390 Round 4: 1001 peptides, 156 chains. Longest chain 25 peptides. Score 0.414 Round 5: 999 peptides, 158 chains. Longest chain 17 peptides. Score 0.408 Taking the results from Round 4 Chains 158, Residues 845, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 22829 reflections ( 97.72 % complete ) and 39911 restraints for refining 17077 atoms. 36637 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1728 (Rfree = 0.000) for 17077 atoms. Found 34 (81 requested) and removed 91 (40 requested) atoms. Cycle 32: After refmac, R = 0.1732 (Rfree = 0.000) for 16938 atoms. Found 63 (80 requested) and removed 76 (40 requested) atoms. Cycle 33: After refmac, R = 0.1652 (Rfree = 0.000) for 16886 atoms. Found 66 (80 requested) and removed 74 (40 requested) atoms. Cycle 34: After refmac, R = 0.1256 (Rfree = 0.000) for 16835 atoms. Found 14 (80 requested) and removed 54 (40 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1188 (Rfree = 0.000) for 16779 atoms. Found 12 (79 requested) and removed 47 (39 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.94 3.69 Search for helices and strands: 0 residues in 0 chains, 17287 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 17304 seeds are put forward Round 1: 856 peptides, 173 chains. Longest chain 10 peptides. Score 0.281 Round 2: 989 peptides, 164 chains. Longest chain 16 peptides. Score 0.387 Round 3: 959 peptides, 161 chains. Longest chain 16 peptides. Score 0.377 Round 4: 998 peptides, 160 chains. Longest chain 19 peptides. Score 0.402 Round 5: 970 peptides, 155 chains. Longest chain 16 peptides. Score 0.399 Taking the results from Round 4 Chains 161, Residues 838, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39895 restraints for refining 17076 atoms. 36575 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1792 (Rfree = 0.000) for 17076 atoms. Found 53 (81 requested) and removed 82 (40 requested) atoms. Cycle 37: After refmac, R = 0.1736 (Rfree = 0.000) for 16978 atoms. Found 80 (80 requested) and removed 61 (40 requested) atoms. Cycle 38: After refmac, R = 0.1606 (Rfree = 0.000) for 16966 atoms. Found 49 (80 requested) and removed 59 (40 requested) atoms. Cycle 39: After refmac, R = 0.1612 (Rfree = 0.000) for 16924 atoms. Found 61 (80 requested) and removed 67 (40 requested) atoms. Cycle 40: After refmac, R = 0.1545 (Rfree = 0.000) for 16898 atoms. Found 78 (80 requested) and removed 55 (40 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.95 3.69 Search for helices and strands: 0 residues in 0 chains, 17408 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 17425 seeds are put forward Round 1: 739 peptides, 152 chains. Longest chain 11 peptides. Score 0.262 Round 2: 841 peptides, 151 chains. Longest chain 15 peptides. Score 0.332 Round 3: 837 peptides, 147 chains. Longest chain 15 peptides. Score 0.340 Round 4: 871 peptides, 146 chains. Longest chain 15 peptides. Score 0.364 Round 5: 872 peptides, 144 chains. Longest chain 14 peptides. Score 0.370 Taking the results from Round 5 Chains 145, Residues 728, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 41254 restraints for refining 17078 atoms. 38449 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1801 (Rfree = 0.000) for 17078 atoms. Found 62 (81 requested) and removed 74 (40 requested) atoms. Cycle 42: After refmac, R = 0.1713 (Rfree = 0.000) for 16994 atoms. Found 81 (81 requested) and removed 75 (40 requested) atoms. Cycle 43: After refmac, R = 0.1675 (Rfree = 0.000) for 16965 atoms. Found 80 (80 requested) and removed 76 (40 requested) atoms. Cycle 44: After refmac, R = 0.1594 (Rfree = 0.000) for 16945 atoms. Found 80 (80 requested) and removed 57 (40 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1581 (Rfree = 0.000) for 16943 atoms. Found 75 (80 requested) and removed 60 (40 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.93 3.68 Search for helices and strands: 0 residues in 0 chains, 17421 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 17436 seeds are put forward Round 1: 742 peptides, 159 chains. Longest chain 11 peptides. Score 0.244 Round 2: 828 peptides, 155 chains. Longest chain 14 peptides. Score 0.312 Round 3: 845 peptides, 149 chains. Longest chain 16 peptides. Score 0.339 Round 4: 845 peptides, 151 chains. Longest chain 16 peptides. Score 0.334 Round 5: 833 peptides, 140 chains. Longest chain 17 peptides. Score 0.357 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 141, Residues 693, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2prr-4_warpNtrace.pdb as input Building loops using Loopy2018 141 chains (693 residues) following loop building 3 chains (18 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22829 reflections ( 97.72 % complete ) and 40838 restraints for refining 17078 atoms. 38139 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1714 (Rfree = 0.000) for 17078 atoms. Found 0 (81 requested) and removed 40 (40 requested) atoms. Cycle 47: After refmac, R = 0.1724 (Rfree = 0.000) for 16977 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 48: After refmac, R = 0.1691 (Rfree = 0.000) for 16904 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 49: After refmac, R = 0.1640 (Rfree = 0.000) for 16830 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Writing output files ... TimeTaking 154.38