Mon 24 Dec 00:30:36 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 2prx-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2prx-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2prx-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-2.0-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/2prx-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-2.0-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 00:30:40 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/2prx-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2prx-2.0-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 296 and 0 Target number of residues in the AU: 296 Target solvent content: 0.4551 Checking the provided sequence file Detected sequence length: 160 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 320 Adjusted target solvent content: 0.41 Input MTZ file: 2prx-2.0-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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-2.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2560 target number of atoms Had to go as low as 0.60 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: 28.816 2.000 Wilson plot Bfac: 15.36 19184 reflections ( 99.72 % complete ) and 0 restraints for refining 2844 atoms. Observations/parameters ratio is 1.69 ------------------------------------------------------ Starting model: R = 0.3397 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3004 (Rfree = 0.000) for 2844 atoms. Found 56 (97 requested) and removed 53 (48 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.86 2.10 NCS extension: 0 residues added, 2847 seeds are put forward Round 1: 139 peptides, 27 chains. Longest chain 8 peptides. Score 0.353 Round 2: 168 peptides, 24 chains. Longest chain 16 peptides. Score 0.560 Round 3: 188 peptides, 25 chains. Longest chain 20 peptides. Score 0.623 Round 4: 199 peptides, 24 chains. Longest chain 23 peptides. Score 0.678 Round 5: 207 peptides, 21 chains. Longest chain 28 peptides. Score 0.744 Taking the results from Round 5 Chains 22, Residues 186, Estimated correctness of the model 94.1 % 3 chains (33 residues) have been docked in sequence Building loops using Loopy2018 22 chains (186 residues) following loop building 3 chains (33 residues) in sequence following loop building ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 4462 restraints for refining 2483 atoms. 3651 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3199 (Rfree = 0.000) for 2483 atoms. Found 78 (85 requested) and removed 42 (42 requested) atoms. Cycle 2: After refmac, R = 0.2936 (Rfree = 0.000) for 2516 atoms. Found 56 (84 requested) and removed 21 (43 requested) atoms. Cycle 3: After refmac, R = 0.2786 (Rfree = 0.000) for 2546 atoms. Found 61 (85 requested) and removed 7 (43 requested) atoms. Cycle 4: After refmac, R = 0.2645 (Rfree = 0.000) for 2596 atoms. Found 57 (87 requested) and removed 10 (44 requested) atoms. Cycle 5: After refmac, R = 0.2536 (Rfree = 0.000) for 2642 atoms. Found 43 (88 requested) and removed 6 (45 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.83 2.07 NCS extension: 8 residues added (4 deleted due to clashes), 2702 seeds are put forward Round 1: 182 peptides, 23 chains. Longest chain 22 peptides. Score 0.634 Round 2: 188 peptides, 20 chains. Longest chain 30 peptides. Score 0.702 Round 3: 200 peptides, 19 chains. Longest chain 33 peptides. Score 0.750 Round 4: 195 peptides, 19 chains. Longest chain 32 peptides. Score 0.737 Round 5: 188 peptides, 17 chains. Longest chain 33 peptides. Score 0.744 Taking the results from Round 3 Chains 22, Residues 181, Estimated correctness of the model 94.4 % 2 chains (36 residues) have been docked in sequence Building loops using Loopy2018 22 chains (181 residues) following loop building 2 chains (36 residues) in sequence following loop building ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 4840 restraints for refining 2649 atoms. 4010 conditional restraints added. Observations/parameters ratio is 1.81 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2668 (Rfree = 0.000) for 2649 atoms. Found 75 (88 requested) and removed 45 (45 requested) atoms. Cycle 7: After refmac, R = 0.2512 (Rfree = 0.000) for 2679 atoms. Found 59 (87 requested) and removed 7 (45 requested) atoms. Cycle 8: After refmac, R = 0.2396 (Rfree = 0.000) for 2731 atoms. Found 49 (89 requested) and removed 7 (46 requested) atoms. Cycle 9: After refmac, R = 0.2304 (Rfree = 0.000) for 2773 atoms. Found 35 (90 requested) and removed 7 (47 requested) atoms. Cycle 10: After refmac, R = 0.2249 (Rfree = 0.000) for 2797 atoms. Found 47 (91 requested) and removed 8 (47 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.81 2.04 NCS extension: 18 residues added (7 deleted due to clashes), 2861 seeds are put forward Round 1: 184 peptides, 22 chains. Longest chain 26 peptides. Score 0.658 Round 2: 191 peptides, 18 chains. Longest chain 30 peptides. Score 0.739 Round 3: 191 peptides, 18 chains. Longest chain 21 peptides. Score 0.739 Round 4: 196 peptides, 19 chains. Longest chain 31 peptides. Score 0.739 Round 5: 188 peptides, 19 chains. Longest chain 20 peptides. Score 0.716 Taking the results from Round 4 Chains 20, Residues 177, Estimated correctness of the model 93.9 % 2 chains (21 residues) have been docked in sequence Building loops using Loopy2018 20 chains (177 residues) following loop building 2 chains (21 residues) in sequence following loop building ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 5276 restraints for refining 2762 atoms. 4521 conditional restraints added. Observations/parameters ratio is 1.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2436 (Rfree = 0.000) for 2762 atoms. Found 89 (90 requested) and removed 29 (47 requested) atoms. Cycle 12: After refmac, R = 0.2273 (Rfree = 0.000) for 2822 atoms. Found 53 (92 requested) and removed 7 (48 requested) atoms. Cycle 13: After refmac, R = 0.2152 (Rfree = 0.000) for 2866 atoms. Found 52 (94 requested) and removed 4 (49 requested) atoms. Cycle 14: After refmac, R = 0.2051 (Rfree = 0.000) for 2912 atoms. Found 41 (95 requested) and removed 3 (49 requested) atoms. Cycle 15: After refmac, R = 0.1994 (Rfree = 0.000) for 2949 atoms. Found 34 (97 requested) and removed 7 (50 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.80 2.03 NCS extension: 0 residues added, 2980 seeds are put forward Round 1: 181 peptides, 21 chains. Longest chain 26 peptides. Score 0.663 Round 2: 188 peptides, 18 chains. Longest chain 27 peptides. Score 0.730 Round 3: 178 peptides, 19 chains. Longest chain 19 peptides. Score 0.684 Round 4: 184 peptides, 19 chains. Longest chain 25 peptides. Score 0.704 Round 5: 180 peptides, 19 chains. Longest chain 24 peptides. Score 0.691 Taking the results from Round 2 Chains 22, Residues 170, Estimated correctness of the model 93.5 % 3 chains (44 residues) have been docked in sequence Building loops using Loopy2018 22 chains (170 residues) following loop building 3 chains (44 residues) in sequence following loop building ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 5472 restraints for refining 2933 atoms. 4651 conditional restraints added. Observations/parameters ratio is 1.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2197 (Rfree = 0.000) for 2933 atoms. Found 83 (96 requested) and removed 46 (50 requested) atoms. Cycle 17: After refmac, R = 0.2050 (Rfree = 0.000) for 2969 atoms. Found 56 (95 requested) and removed 8 (50 requested) atoms. Cycle 18: After refmac, R = 0.1948 (Rfree = 0.000) for 3016 atoms. Found 45 (97 requested) and removed 8 (51 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1883 (Rfree = 0.000) for 3051 atoms. Found 41 (98 requested) and removed 6 (52 requested) atoms. Cycle 20: After refmac, R = 0.1823 (Rfree = 0.000) for 3085 atoms. Found 39 (99 requested) and removed 11 (52 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.81 2.04 NCS extension: 8 residues added (5 deleted due to clashes), 3127 seeds are put forward Round 1: 151 peptides, 19 chains. Longest chain 24 peptides. Score 0.583 Round 2: 168 peptides, 18 chains. Longest chain 31 peptides. Score 0.666 Round 3: 168 peptides, 17 chains. Longest chain 24 peptides. Score 0.682 Round 4: 169 peptides, 18 chains. Longest chain 26 peptides. Score 0.670 Round 5: 174 peptides, 18 chains. Longest chain 31 peptides. Score 0.687 Taking the results from Round 5 Chains 19, Residues 156, Estimated correctness of the model 91.5 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 5911 restraints for refining 2978 atoms. 5228 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2100 (Rfree = 0.000) for 2978 atoms. Found 96 (96 requested) and removed 24 (51 requested) atoms. Cycle 22: After refmac, R = 0.1940 (Rfree = 0.000) for 3049 atoms. Found 74 (98 requested) and removed 9 (52 requested) atoms. Cycle 23: After refmac, R = 0.1868 (Rfree = 0.000) for 3113 atoms. Found 55 (100 requested) and removed 19 (53 requested) atoms. Cycle 24: After refmac, R = 0.1832 (Rfree = 0.000) for 3144 atoms. Found 54 (101 requested) and removed 20 (53 requested) atoms. Cycle 25: After refmac, R = 0.1804 (Rfree = 0.000) for 3178 atoms. Found 38 (102 requested) and removed 18 (54 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.81 2.04 NCS extension: 3 residues added (0 deleted due to clashes), 3205 seeds are put forward Round 1: 160 peptides, 20 chains. Longest chain 17 peptides. Score 0.601 Round 2: 174 peptides, 19 chains. Longest chain 24 peptides. Score 0.671 Round 3: 179 peptides, 17 chains. Longest chain 25 peptides. Score 0.718 Round 4: 178 peptides, 17 chains. Longest chain 27 peptides. Score 0.715 Round 5: 175 peptides, 17 chains. Longest chain 27 peptides. Score 0.705 Taking the results from Round 3 Chains 17, Residues 162, Estimated correctness of the model 93.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6210 restraints for refining 3040 atoms. 5579 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1981 (Rfree = 0.000) for 3040 atoms. Found 98 (98 requested) and removed 5 (52 requested) atoms. Cycle 27: After refmac, R = 0.1849 (Rfree = 0.000) for 3132 atoms. Found 75 (101 requested) and removed 4 (53 requested) atoms. Cycle 28: After refmac, R = 0.1760 (Rfree = 0.000) for 3203 atoms. Found 50 (102 requested) and removed 12 (54 requested) atoms. Cycle 29: After refmac, R = 0.1701 (Rfree = 0.000) for 3240 atoms. Found 41 (104 requested) and removed 18 (55 requested) atoms. Cycle 30: After refmac, R = 0.1679 (Rfree = 0.000) for 3260 atoms. Found 56 (104 requested) and removed 17 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.82 2.05 NCS extension: 6 residues added (5 deleted due to clashes), 3307 seeds are put forward Round 1: 148 peptides, 18 chains. Longest chain 17 peptides. Score 0.589 Round 2: 168 peptides, 17 chains. Longest chain 26 peptides. Score 0.682 Round 3: 174 peptides, 19 chains. Longest chain 27 peptides. Score 0.671 Round 4: 171 peptides, 17 chains. Longest chain 26 peptides. Score 0.692 Round 5: 169 peptides, 19 chains. Longest chain 25 peptides. Score 0.653 Taking the results from Round 4 Chains 19, Residues 154, Estimated correctness of the model 91.8 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6310 restraints for refining 3150 atoms. 5600 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1971 (Rfree = 0.000) for 3150 atoms. Found 101 (101 requested) and removed 38 (53 requested) atoms. Cycle 32: After refmac, R = 0.1824 (Rfree = 0.000) for 3212 atoms. Found 81 (103 requested) and removed 12 (55 requested) atoms. Cycle 33: After refmac, R = 0.1737 (Rfree = 0.000) for 3280 atoms. Found 77 (105 requested) and removed 15 (56 requested) atoms. Cycle 34: After refmac, R = 0.1677 (Rfree = 0.000) for 3342 atoms. Found 60 (107 requested) and removed 37 (57 requested) atoms. Cycle 35: After refmac, R = 0.1647 (Rfree = 0.000) for 3362 atoms. Found 74 (108 requested) and removed 40 (57 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.81 2.04 NCS extension: 0 residues added, 3398 seeds are put forward Round 1: 155 peptides, 20 chains. Longest chain 17 peptides. Score 0.581 Round 2: 164 peptides, 18 chains. Longest chain 23 peptides. Score 0.652 Round 3: 166 peptides, 19 chains. Longest chain 23 peptides. Score 0.642 Round 4: 172 peptides, 16 chains. Longest chain 23 peptides. Score 0.711 Round 5: 173 peptides, 19 chains. Longest chain 24 peptides. Score 0.667 Taking the results from Round 4 Chains 19, Residues 156, Estimated correctness of the model 92.7 % 2 chains (24 residues) have been docked in sequence Building loops using Loopy2018 19 chains (156 residues) following loop building 2 chains (24 residues) in sequence following loop building ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6635 restraints for refining 3218 atoms. 5948 conditional restraints added. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1959 (Rfree = 0.000) for 3218 atoms. Found 103 (103 requested) and removed 40 (55 requested) atoms. Cycle 37: After refmac, R = 0.1804 (Rfree = 0.000) for 3278 atoms. Found 96 (105 requested) and removed 9 (56 requested) atoms. Cycle 38: After refmac, R = 0.1718 (Rfree = 0.000) for 3363 atoms. Found 53 (108 requested) and removed 27 (57 requested) atoms. Cycle 39: After refmac, R = 0.1656 (Rfree = 0.000) for 3385 atoms. Found 71 (107 requested) and removed 11 (58 requested) atoms. Cycle 40: After refmac, R = 0.1625 (Rfree = 0.000) for 3444 atoms. Found 42 (109 requested) and removed 37 (59 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.82 2.05 NCS extension: 24 residues added (5 deleted due to clashes), 3478 seeds are put forward Round 1: 162 peptides, 19 chains. Longest chain 22 peptides. Score 0.627 Round 2: 171 peptides, 21 chains. Longest chain 18 peptides. Score 0.627 Round 3: 168 peptides, 19 chains. Longest chain 19 peptides. Score 0.650 Round 4: 175 peptides, 19 chains. Longest chain 29 peptides. Score 0.674 Round 5: 168 peptides, 17 chains. Longest chain 23 peptides. Score 0.682 Taking the results from Round 5 Chains 18, Residues 151, Estimated correctness of the model 91.3 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6794 restraints for refining 3218 atoms. 6182 conditional restraints added. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1930 (Rfree = 0.000) for 3218 atoms. Found 99 (99 requested) and removed 19 (55 requested) atoms. Cycle 42: After refmac, R = 0.1803 (Rfree = 0.000) for 3297 atoms. Found 94 (101 requested) and removed 4 (56 requested) atoms. Cycle 43: After refmac, R = 0.1693 (Rfree = 0.000) for 3386 atoms. Found 49 (104 requested) and removed 25 (58 requested) atoms. Cycle 44: After refmac, R = 0.1654 (Rfree = 0.000) for 3408 atoms. Found 48 (104 requested) and removed 27 (58 requested) atoms. Cycle 45: After refmac, R = 0.1623 (Rfree = 0.000) for 3428 atoms. Found 56 (105 requested) and removed 35 (58 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.81 2.04 NCS extension: 3 residues added (4 deleted due to clashes), 3456 seeds are put forward Round 1: 157 peptides, 19 chains. Longest chain 23 peptides. Score 0.608 Round 2: 153 peptides, 17 chains. Longest chain 22 peptides. Score 0.628 Round 3: 155 peptides, 15 chains. Longest chain 23 peptides. Score 0.670 Round 4: 160 peptides, 18 chains. Longest chain 22 peptides. Score 0.637 Round 5: 176 peptides, 16 chains. Longest chain 24 peptides. Score 0.723 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 160, Estimated correctness of the model 93.2 % 2 chains (32 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 2prx-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 44 A and 52 A 16 chains (166 residues) following loop building 1 chains (39 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19184 reflections ( 99.72 % complete ) and 6508 restraints for refining 3304 atoms. 5722 conditional restraints added. Observations/parameters ratio is 1.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2053 (Rfree = 0.000) for 3304 atoms. Found 0 (102 requested) and removed 1 (56 requested) atoms. Cycle 47: After refmac, R = 0.1960 (Rfree = 0.000) for 3303 atoms. Found 0 (99 requested) and removed 0 (56 requested) atoms. Cycle 48: After refmac, R = 0.1920 (Rfree = 0.000) for 3303 atoms. Found 0 (99 requested) and removed 1 (56 requested) atoms. Cycle 49: After refmac, R = 0.1898 (Rfree = 0.000) for 3302 atoms. Found 0 (97 requested) and removed 1 (56 requested) atoms. Writing output files ... TimeTaking 33.07