Sun 23 Dec 22:22:56 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 2pg4-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pg4-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-2.2-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/2pg4-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-2.2-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 22:23:05 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/2pg4-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pg4-2.2-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 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-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: 90 Cell parameters: 109.840 109.840 36.760 90.000 90.000 90.000 Input sequence file: 2pg4-2.2-parrot-hancs.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 1679 atoms. Observations/parameters ratio is 1.75 ------------------------------------------------------ Starting model: R = 0.3947 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3635 (Rfree = 0.000) for 1679 atoms. Found 24 (44 requested) and removed 27 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.81 2.66 NCS extension: 0 residues added, 1676 seeds are put forward Round 1: 95 peptides, 18 chains. Longest chain 9 peptides. Score 0.353 Round 2: 109 peptides, 16 chains. Longest chain 16 peptides. Score 0.510 Round 3: 126 peptides, 15 chains. Longest chain 22 peptides. Score 0.631 Round 4: 126 peptides, 15 chains. Longest chain 17 peptides. Score 0.631 Round 5: 128 peptides, 16 chains. Longest chain 19 peptides. Score 0.618 Taking the results from Round 4 Chains 16, Residues 111, Estimated correctness of the model 84.6 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2926 restraints for refining 1452 atoms. 2458 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3810 (Rfree = 0.000) for 1452 atoms. Found 15 (38 requested) and removed 26 (19 requested) atoms. Cycle 2: After refmac, R = 0.3617 (Rfree = 0.000) for 1432 atoms. Found 12 (37 requested) and removed 22 (18 requested) atoms. Cycle 3: After refmac, R = 0.3669 (Rfree = 0.000) for 1412 atoms. Found 15 (37 requested) and removed 21 (18 requested) atoms. Cycle 4: After refmac, R = 0.3508 (Rfree = 0.000) for 1403 atoms. Found 14 (36 requested) and removed 19 (18 requested) atoms. Cycle 5: After refmac, R = 0.3615 (Rfree = 0.000) for 1392 atoms. Found 8 (36 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.61 2.47 NCS extension: 11 residues added (2 deleted due to clashes), 1400 seeds are put forward Round 1: 124 peptides, 17 chains. Longest chain 16 peptides. Score 0.572 Round 2: 139 peptides, 13 chains. Longest chain 27 peptides. Score 0.730 Round 3: 127 peptides, 10 chains. Longest chain 29 peptides. Score 0.740 Round 4: 140 peptides, 11 chains. Longest chain 41 peptides. Score 0.769 Round 5: 135 peptides, 13 chains. Longest chain 29 peptides. Score 0.714 Taking the results from Round 4 Chains 13, Residues 129, Estimated correctness of the model 93.5 % 4 chains (69 residues) have been docked in sequence Building loops using Loopy2018 13 chains (129 residues) following loop building 4 chains (69 residues) in sequence following loop building ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2243 restraints for refining 1452 atoms. 1481 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3781 (Rfree = 0.000) for 1452 atoms. Found 17 (38 requested) and removed 25 (19 requested) atoms. Cycle 7: After refmac, R = 0.3561 (Rfree = 0.000) for 1436 atoms. Found 14 (36 requested) and removed 18 (18 requested) atoms. Cycle 8: After refmac, R = 0.3435 (Rfree = 0.000) for 1429 atoms. Found 14 (36 requested) and removed 18 (18 requested) atoms. Cycle 9: After refmac, R = 0.3379 (Rfree = 0.000) for 1417 atoms. Found 12 (35 requested) and removed 18 (18 requested) atoms. Cycle 10: After refmac, R = 0.3295 (Rfree = 0.000) for 1410 atoms. Found 8 (34 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.59 2.46 NCS extension: 41 residues added (6 deleted due to clashes), 1444 seeds are put forward Round 1: 127 peptides, 13 chains. Longest chain 20 peptides. Score 0.680 Round 2: 126 peptides, 10 chains. Longest chain 41 peptides. Score 0.736 Round 3: 130 peptides, 9 chains. Longest chain 41 peptides. Score 0.769 Round 4: 125 peptides, 11 chains. Longest chain 29 peptides. Score 0.712 Round 5: 125 peptides, 7 chains. Longest chain 49 peptides. Score 0.787 Taking the results from Round 5 Chains 9, Residues 118, Estimated correctness of the model 94.4 % 2 chains (41 residues) have been docked in sequence Building loops using Loopy2018 9 chains (118 residues) following loop building 2 chains (41 residues) in sequence following loop building ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2487 restraints for refining 1436 atoms. 1860 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3491 (Rfree = 0.000) for 1436 atoms. Found 20 (33 requested) and removed 19 (18 requested) atoms. Cycle 12: After refmac, R = 0.3371 (Rfree = 0.000) for 1432 atoms. Found 11 (33 requested) and removed 19 (18 requested) atoms. Cycle 13: After refmac, R = 0.3193 (Rfree = 0.000) for 1421 atoms. Found 17 (32 requested) and removed 18 (18 requested) atoms. Cycle 14: After refmac, R = 0.3137 (Rfree = 0.000) for 1418 atoms. Found 12 (31 requested) and removed 17 (18 requested) atoms. Cycle 15: After refmac, R = 0.3051 (Rfree = 0.000) for 1413 atoms. Found 8 (30 requested) and removed 15 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.51 2.38 NCS extension: 33 residues added (6 deleted due to clashes), 1440 seeds are put forward Round 1: 114 peptides, 12 chains. Longest chain 22 peptides. Score 0.640 Round 2: 124 peptides, 8 chains. Longest chain 42 peptides. Score 0.766 Round 3: 116 peptides, 10 chains. Longest chain 42 peptides. Score 0.694 Round 4: 126 peptides, 7 chains. Longest chain 42 peptides. Score 0.790 Round 5: 118 peptides, 8 chains. Longest chain 42 peptides. Score 0.744 Taking the results from Round 4 Chains 10, Residues 119, Estimated correctness of the model 94.5 % 2 chains (40 residues) have been docked in sequence Building loops using Loopy2018 10 chains (119 residues) following loop building 2 chains (40 residues) in sequence following loop building ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2426 restraints for refining 1438 atoms. 1796 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3368 (Rfree = 0.000) for 1438 atoms. Found 13 (30 requested) and removed 19 (18 requested) atoms. Cycle 17: After refmac, R = 0.3211 (Rfree = 0.000) for 1432 atoms. Found 12 (29 requested) and removed 18 (18 requested) atoms. Cycle 18: After refmac, R = 0.3110 (Rfree = 0.000) for 1425 atoms. Found 12 (28 requested) and removed 4 (18 requested) atoms. Cycle 19: After refmac, R = 0.3061 (Rfree = 0.000) for 1433 atoms. Found 15 (28 requested) and removed 9 (18 requested) atoms. Cycle 20: After refmac, R = 0.3000 (Rfree = 0.000) for 1438 atoms. Found 12 (27 requested) and removed 12 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.49 2.36 NCS extension: 39 residues added (5 deleted due to clashes), 1479 seeds are put forward Round 1: 117 peptides, 9 chains. Longest chain 33 peptides. Score 0.720 Round 2: 128 peptides, 9 chains. Longest chain 35 peptides. Score 0.762 Round 3: 139 peptides, 12 chains. Longest chain 25 peptides. Score 0.748 Round 4: 136 peptides, 14 chains. Longest chain 33 peptides. Score 0.699 Round 5: 141 peptides, 12 chains. Longest chain 36 peptides. Score 0.755 Taking the results from Round 2 Chains 12, Residues 119, Estimated correctness of the model 93.1 % 3 chains (45 residues) have been docked in sequence Building loops using Loopy2018 12 chains (119 residues) following loop building 3 chains (45 residues) in sequence following loop building ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2404 restraints for refining 1452 atoms. 1771 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3183 (Rfree = 0.000) for 1452 atoms. Found 21 (27 requested) and removed 19 (19 requested) atoms. Cycle 22: After refmac, R = 0.3067 (Rfree = 0.000) for 1451 atoms. Found 17 (27 requested) and removed 14 (19 requested) atoms. Cycle 23: After refmac, R = 0.2991 (Rfree = 0.000) for 1453 atoms. Found 10 (26 requested) and removed 10 (19 requested) atoms. Cycle 24: After refmac, R = 0.2957 (Rfree = 0.000) for 1453 atoms. Found 5 (25 requested) and removed 8 (19 requested) atoms. Cycle 25: After refmac, R = 0.2926 (Rfree = 0.000) for 1449 atoms. Found 3 (24 requested) and removed 4 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.49 2.36 NCS extension: 38 residues added (2 deleted due to clashes), 1487 seeds are put forward Round 1: 131 peptides, 12 chains. Longest chain 25 peptides. Score 0.717 Round 2: 137 peptides, 12 chains. Longest chain 25 peptides. Score 0.741 Round 3: 142 peptides, 8 chains. Longest chain 37 peptides. Score 0.822 Round 4: 141 peptides, 8 chains. Longest chain 38 peptides. Score 0.819 Round 5: 144 peptides, 11 chains. Longest chain 28 peptides. Score 0.782 Taking the results from Round 3 Chains 10, Residues 134, Estimated correctness of the model 95.9 % 3 chains (74 residues) have been docked in sequence Building loops using Loopy2018 10 chains (134 residues) following loop building 3 chains (74 residues) in sequence following loop building ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2103 restraints for refining 1507 atoms. 1281 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3301 (Rfree = 0.000) for 1507 atoms. Found 14 (24 requested) and removed 24 (19 requested) atoms. Cycle 27: After refmac, R = 0.3076 (Rfree = 0.000) for 1496 atoms. Found 12 (23 requested) and removed 19 (19 requested) atoms. Cycle 28: After refmac, R = 0.2978 (Rfree = 0.000) for 1487 atoms. Found 7 (23 requested) and removed 14 (19 requested) atoms. Cycle 29: After refmac, R = 0.2934 (Rfree = 0.000) for 1479 atoms. Found 8 (21 requested) and removed 8 (19 requested) atoms. Cycle 30: After refmac, R = 0.2872 (Rfree = 0.000) for 1478 atoms. Found 9 (21 requested) and removed 4 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.55 2.42 NCS extension: 35 residues added (12 deleted due to clashes), 1521 seeds are put forward Round 1: 131 peptides, 9 chains. Longest chain 26 peptides. Score 0.772 Round 2: 134 peptides, 11 chains. Longest chain 23 peptides. Score 0.747 Round 3: 139 peptides, 13 chains. Longest chain 36 peptides. Score 0.730 Round 4: 140 peptides, 10 chains. Longest chain 24 peptides. Score 0.785 Round 5: 144 peptides, 12 chains. Longest chain 32 peptides. Score 0.765 Taking the results from Round 4 Chains 10, Residues 130, Estimated correctness of the model 94.3 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2505 restraints for refining 1452 atoms. 1905 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3125 (Rfree = 0.000) for 1452 atoms. Found 17 (21 requested) and removed 19 (19 requested) atoms. Cycle 32: After refmac, R = 0.2952 (Rfree = 0.000) for 1450 atoms. Found 15 (20 requested) and removed 13 (19 requested) atoms. Cycle 33: After refmac, R = 0.2858 (Rfree = 0.000) for 1452 atoms. Found 13 (19 requested) and removed 8 (19 requested) atoms. Cycle 34: After refmac, R = 0.2780 (Rfree = 0.000) for 1457 atoms. Found 4 (19 requested) and removed 3 (19 requested) atoms. Cycle 35: After refmac, R = 0.2758 (Rfree = 0.000) for 1456 atoms. Found 1 (19 requested) and removed 2 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.53 2.40 NCS extension: 11 residues added (10 deleted due to clashes), 1467 seeds are put forward Round 1: 138 peptides, 11 chains. Longest chain 23 peptides. Score 0.762 Round 2: 133 peptides, 10 chains. Longest chain 31 peptides. Score 0.762 Round 3: 141 peptides, 10 chains. Longest chain 31 peptides. Score 0.788 Round 4: 135 peptides, 12 chains. Longest chain 31 peptides. Score 0.733 Round 5: 136 peptides, 11 chains. Longest chain 31 peptides. Score 0.755 Taking the results from Round 3 Chains 11, Residues 131, Estimated correctness of the model 94.4 % 3 chains (57 residues) have been docked in sequence Building loops using Loopy2018 11 chains (131 residues) following loop building 3 chains (57 residues) in sequence following loop building ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2182 restraints for refining 1455 atoms. 1429 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2975 (Rfree = 0.000) for 1455 atoms. Found 19 (19 requested) and removed 20 (19 requested) atoms. Cycle 37: After refmac, R = 0.2816 (Rfree = 0.000) for 1454 atoms. Found 11 (19 requested) and removed 12 (19 requested) atoms. Cycle 38: After refmac, R = 0.2754 (Rfree = 0.000) for 1451 atoms. Found 9 (19 requested) and removed 7 (19 requested) atoms. Cycle 39: After refmac, R = 0.2703 (Rfree = 0.000) for 1452 atoms. Found 10 (19 requested) and removed 4 (19 requested) atoms. Cycle 40: After refmac, R = 0.2684 (Rfree = 0.000) for 1458 atoms. Found 5 (19 requested) and removed 2 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.48 2.35 NCS extension: 25 residues added (7 deleted due to clashes), 1488 seeds are put forward Round 1: 145 peptides, 10 chains. Longest chain 38 peptides. Score 0.800 Round 2: 148 peptides, 9 chains. Longest chain 41 peptides. Score 0.823 Round 3: 151 peptides, 8 chains. Longest chain 50 peptides. Score 0.844 Round 4: 150 peptides, 9 chains. Longest chain 45 peptides. Score 0.829 Round 5: 145 peptides, 10 chains. Longest chain 32 peptides. Score 0.800 Taking the results from Round 3 Chains 8, Residues 143, Estimated correctness of the model 96.8 % 2 chains (71 residues) have been docked in sequence Building loops using Loopy2018 8 chains (143 residues) following loop building 2 chains (71 residues) in sequence following loop building ------------------------------------------------------ 11724 reflections ( 98.80 % complete ) and 2005 restraints for refining 1459 atoms. 1144 conditional restraints added. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2903 (Rfree = 0.000) for 1459 atoms. Found 19 (19 requested) and removed 21 (19 requested) atoms. Cycle 42: After refmac, R = 0.2756 (Rfree = 0.000) for 1457 atoms. Found 9 (19 requested) and removed 9 (19 requested) atoms. Cycle 43: After refmac, R = 0.2698 (Rfree = 0.000) for 1455 atoms. Found 6 (19 requested) and removed 5 (19 requested) atoms. Cycle 44: After refmac, R = 0.2671 (Rfree = 0.000) for 1455 atoms. Found 5 (19 requested) and removed 7 (19 requested) atoms. Cycle 45: After refmac, R = 0.2649 (Rfree = 0.000) for 1452 atoms. Found 5 (19 requested) and removed 3 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.51 2.38 NCS extension: 33 residues added (12 deleted due to clashes), 1488 seeds are put forward Round 1: 153 peptides, 8 chains. Longest chain 45 peptides. Score 0.849 Round 2: 151 peptides, 8 chains. Longest chain 45 peptides. Score 0.844 Round 3: 150 peptides, 10 chains. Longest chain 28 peptides. Score 0.815 Round 4: 154 peptides, 8 chains. Longest chain 46 peptides. Score 0.851 Round 5: 151 peptides, 9 chains. Longest chain 30 peptides. Score 0.831 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 146, Estimated correctness of the model 97.1 % 2 chains (60 residues) have been docked in sequence Sequence coverage is 40 % Consider running further cycles of model building using 2pg4-2_warpNtrace.pdb as input Building loops using Loopy2018 8 chains (146 residues) following loop building 2 chains (60 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11724 reflections ( 98.80 % complete ) and 2095 restraints for refining 1452 atoms. 1265 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2796 (Rfree = 0.000) for 1452 atoms. Found 0 (19 requested) and removed 3 (19 requested) atoms. Cycle 47: After refmac, R = 0.2698 (Rfree = 0.000) for 1446 atoms. Found 0 (19 requested) and removed 2 (19 requested) atoms. Cycle 48: After refmac, R = 0.2673 (Rfree = 0.000) for 1444 atoms. Found 0 (18 requested) and removed 1 (18 requested) atoms. Cycle 49: After refmac, R = 0.2656 (Rfree = 0.000) for 1443 atoms. TimeTaking 31.8